diff --git a/src/lib/components/chat/Messages/Citations/CitationModal.svelte b/src/lib/components/chat/Messages/Citations/CitationModal.svelte
index 114d4f48d2..3ec9ae21a0 100644
--- a/src/lib/components/chat/Messages/Citations/CitationModal.svelte
+++ b/src/lib/components/chat/Messages/Citations/CitationModal.svelte
@@ -169,7 +169,7 @@
 								></iframe>
 							{:else}
 								<pre class="text-sm dark:text-gray-400 whitespace-pre-line">
-                {document.document}
+                {document.document.trim()}
               </pre>
 							{/if}
 						</div>
diff --git a/src/lib/components/chat/Messages/Markdown.svelte b/src/lib/components/chat/Messages/Markdown.svelte
index b1ca46c79b..b97a31e4f4 100644
--- a/src/lib/components/chat/Messages/Markdown.svelte
+++ b/src/lib/components/chat/Messages/Markdown.svelte
@@ -9,6 +9,8 @@
 	import { mentionExtension } from '$lib/utils/marked/mention-extension';
 
 	import MarkdownTokens from './Markdown/MarkdownTokens.svelte';
+	import footnoteExtension from '$lib/utils/marked/footnote-extension';
+	import citationExtension from '$lib/utils/marked/citation-extension';
 
 	export let id = '';
 	export let content;
@@ -39,6 +41,8 @@
 
 	marked.use(markedKatexExtension(options));
 	marked.use(markedExtension(options));
+	marked.use(citationExtension(options));
+	marked.use(footnoteExtension(options));
 	marked.use(disableSingleTilde);
 	marked.use({
 		extensions: [mentionExtension({ triggerChar: '@' }), mentionExtension({ triggerChar: '#' })]
@@ -47,7 +51,7 @@
 	$: (async () => {
 		if (content) {
 			tokens = marked.lexer(
-				replaceTokens(processResponseContent(content), sourceIds, model?.name, $user?.name)
+				replaceTokens(processResponseContent(content), model?.name, $user?.name)
 			);
 		}
 	})();
@@ -61,6 +65,7 @@
 		{save}
 		{preview}
 		{editCodeBlock}
+		{sourceIds}
 		{topPadding}
 		{onTaskClick}
 		{onSourceClick}
diff --git a/src/lib/components/chat/Messages/Markdown/HTMLToken.svelte b/src/lib/components/chat/Messages/Markdown/HTMLToken.svelte
index fac4fad1de..da9690c631 100644
--- a/src/lib/components/chat/Messages/Markdown/HTMLToken.svelte
+++ b/src/lib/components/chat/Messages/Markdown/HTMLToken.svelte
@@ -3,14 +3,11 @@
 	import type { Token } from 'marked';
 
 	import { WEBUI_BASE_URL } from '$lib/constants';
-	import Source from './Source.svelte';
 	import { settings } from '$lib/stores';
 
 	export let id: string;
 	export let token: Token;
 
-	export let onSourceClick: Function = () => {};
-
 	let html: string | null = null;
 
 	$: if (token.type === 'html' && token?.text) {
@@ -129,8 +126,6 @@
 				}}
 			></iframe>
 		{/if}
-	{:else if token.text.includes(`<source_id`)}
-		<Source {id} {token} onClick={onSourceClick} />
 	{:else if token.text.trim().match(/^<br\s*\/?>$/i)}
 		<br />
 	{:else}
diff --git a/src/lib/components/chat/Messages/Markdown/MarkdownInlineTokens.svelte b/src/lib/components/chat/Messages/Markdown/MarkdownInlineTokens.svelte
index 85ba8740c1..a5e97ed9e8 100644
--- a/src/lib/components/chat/Messages/Markdown/MarkdownInlineTokens.svelte
+++ b/src/lib/components/chat/Messages/Markdown/MarkdownInlineTokens.svelte
@@ -17,10 +17,12 @@
 	import TextToken from './MarkdownInlineTokens/TextToken.svelte';
 	import CodespanToken from './MarkdownInlineTokens/CodespanToken.svelte';
 	import MentionToken from './MarkdownInlineTokens/MentionToken.svelte';
+	import SourceToken from './SourceToken.svelte';
 
 	export let id: string;
 	export let done = true;
 	export let tokens: Token[];
+	export let sourceIds = [];
 	export let onSourceClick: Function = () => {};
 </script>
 
@@ -68,6 +70,17 @@
 		></iframe>
 	{:else if token.type === 'mention'}
 		<MentionToken {token} />
+	{:else if token.type === 'footnote'}
+		{@html DOMPurify.sanitize(
+			`<sup class="footnote-ref footnote-ref-text">${token.escapedText}</sup>`
+		) || ''}
+	{:else if token.type === 'citation'}
+		<SourceToken {id} {token} {sourceIds} onClick={onSourceClick} />
+		<!-- {#if token.ids && token.ids.length > 0}
+			{#each token.ids as sourceId}
+				<Source id={sourceId - 1} title={sourceIds[sourceId - 1]} onClick={onSourceClick} />
+			{/each}
+		{/if} -->
 	{:else if token.type === 'text'}
 		<TextToken {token} {done} />
 	{/if}
diff --git a/src/lib/components/chat/Messages/Markdown/MarkdownTokens.svelte b/src/lib/components/chat/Messages/Markdown/MarkdownTokens.svelte
index 341861b4ff..143fe20541 100644
--- a/src/lib/components/chat/Messages/Markdown/MarkdownTokens.svelte
+++ b/src/lib/components/chat/Messages/Markdown/MarkdownTokens.svelte
@@ -21,7 +21,6 @@
 	import Tooltip from '$lib/components/common/Tooltip.svelte';
 	import Download from '$lib/components/icons/Download.svelte';
 
-	import Source from './Source.svelte';
 	import HtmlToken from './HTMLToken.svelte';
 	import Clipboard from '$lib/components/icons/Clipboard.svelte';
 
@@ -29,6 +28,7 @@
 	export let tokens: Token[];
 	export let top = true;
 	export let attributes = {};
+	export let sourceIds = [];
 
 	export let done = true;
 
@@ -96,6 +96,7 @@
 				id={`${id}-${tokenIdx}-h`}
 				tokens={token.tokens}
 				{done}
+				{sourceIds}
 				{onSourceClick}
 			/>
 		</svelte:element>
@@ -147,6 +148,7 @@
 												id={`${id}-${tokenIdx}-header-${headerIdx}`}
 												tokens={header.tokens}
 												{done}
+												{sourceIds}
 												{onSourceClick}
 											/>
 										</div>
@@ -172,6 +174,7 @@
 												id={`${id}-${tokenIdx}-row-${rowIdx}-${cellIdx}`}
 												tokens={cell.tokens}
 												{done}
+												{sourceIds}
 												{onSourceClick}
 											/>
 										</div>
@@ -348,6 +351,7 @@
 				id={`${id}-${tokenIdx}-p`}
 				tokens={token.tokens ?? []}
 				{done}
+				{sourceIds}
 				{onSourceClick}
 			/>
 		</p>
@@ -359,6 +363,7 @@
 						id={`${id}-${tokenIdx}-t`}
 						tokens={token.tokens}
 						{done}
+						{sourceIds}
 						{onSourceClick}
 					/>
 				{:else}
@@ -370,6 +375,7 @@
 				id={`${id}-${tokenIdx}-p`}
 				tokens={token.tokens ?? []}
 				{done}
+				{sourceIds}
 				{onSourceClick}
 			/>
 		{:else}
diff --git a/src/lib/components/chat/Messages/Markdown/Source.svelte b/src/lib/components/chat/Messages/Markdown/Source.svelte
index b298337320..d48525e070 100644
--- a/src/lib/components/chat/Messages/Markdown/Source.svelte
+++ b/src/lib/components/chat/Messages/Markdown/Source.svelte
@@ -1,23 +1,10 @@
 <script lang="ts">
 	export let id;
-	export let token;
+
+	export let title: string = 'N/A';
+
 	export let onClick: Function = () => {};
 
-	let attributes: Record<string, string | undefined> = {};
-
-	function extractAttributes(input: string): Record<string, string> {
-		const regex = /(\w+)="([^"]*)"/g;
-		let match;
-		let attrs: Record<string, string> = {};
-
-		// Loop through all matches and populate the attributes object
-		while ((match = regex.exec(input)) !== null) {
-			attrs[match[1]] = match[2];
-		}
-
-		return attrs;
-	}
-
 	// Helper function to return only the domain from a URL
 	function getDomain(url: string): string {
 		const domain = url.replace('http://', '').replace('https://', '').split(/[/?#]/)[0];
@@ -44,23 +31,17 @@
 		}
 		return title;
 	};
-
-	$: attributes = extractAttributes(token.text);
 </script>
 
-{#if attributes.title !== 'N/A'}
+{#if title !== 'N/A'}
 	<button
-		class="text-xs font-medium w-fit translate-y-[2px] px-2 py-0.5 dark:bg-white/5 dark:text-white/60 dark:hover:text-white bg-gray-50 text-black/60 hover:text-black transition rounded-lg"
+		class="text-[10px] w-fit translate-y-[2px] px-2 py-0.5 dark:bg-white/5 dark:text-white/80 dark:hover:text-white bg-gray-50 text-black/80 hover:text-black transition rounded-xl"
 		on:click={() => {
-			onClick(id, attributes.data);
+			onClick(id);
 		}}
 	>
 		<span class="line-clamp-1">
-			{getDisplayTitle(
-				decodeURIComponent(attributes.title)
-					? formattedTitle(decodeURIComponent(attributes.title))
-					: ''
-			)}
+			{getDisplayTitle(formattedTitle(decodeURIComponent(title)))}
 		</span>
 	</button>
 {/if}
diff --git a/src/lib/components/chat/Messages/Markdown/SourceToken.svelte b/src/lib/components/chat/Messages/Markdown/SourceToken.svelte
new file mode 100644
index 0000000000..9d0bbcd6ba
--- /dev/null
+++ b/src/lib/components/chat/Messages/Markdown/SourceToken.svelte
@@ -0,0 +1,70 @@
+<script lang="ts">
+	import { LinkPreview } from 'bits-ui';
+	import Source from './Source.svelte';
+
+	export let id;
+	export let token;
+	export let sourceIds = [];
+	export let onClick: Function = () => {};
+
+	let containerElement;
+
+	// Helper function to return only the domain from a URL
+	function getDomain(url: string): string {
+		const domain = url.replace('http://', '').replace('https://', '').split(/[/?#]/)[0];
+
+		if (domain.startsWith('www.')) {
+			return domain.slice(4);
+		}
+		return domain;
+	}
+
+	// Helper function to check if text is a URL and return the domain
+	function formattedTitle(title: string): string {
+		if (title.startsWith('http')) {
+			return getDomain(title);
+		}
+
+		return title;
+	}
+
+	const getDisplayTitle = (title: string) => {
+		if (!title) return 'N/A';
+		if (title.length > 30) {
+			return title.slice(0, 15) + '...' + title.slice(-10);
+		}
+		return title;
+	};
+</script>
+
+{#if (token?.ids ?? []).length == 1}
+	<Source id={token.ids[0] - 1} title={sourceIds[token.ids[0] - 1]} {onClick} />
+{:else}
+	<LinkPreview.Root openDelay={0}>
+		<LinkPreview.Trigger>
+			<button
+				class="text-[10px] w-fit translate-y-[2px] px-2 py-0.5 dark:bg-white/5 dark:text-white/80 dark:hover:text-white bg-gray-50 text-black/80 hover:text-black transition rounded-xl"
+			>
+				<span class="line-clamp-1">
+					{getDisplayTitle(formattedTitle(decodeURIComponent(sourceIds[token.ids[0] - 1])))}
+					<span class="dark:text-white/50 text-black/50">+{(token?.ids ?? []).length - 1}</span>
+				</span>
+			</button>
+		</LinkPreview.Trigger>
+		<LinkPreview.Content
+			class="z-[999]"
+			align="start"
+			strategy="fixed"
+			sideOffset={6}
+			el={containerElement}
+		>
+			<div class="bg-gray-50 dark:bg-gray-850 rounded-xl p-1 cursor-pointer">
+				{#each token.ids as sourceId}
+					<div class="">
+						<Source id={sourceId - 1} title={sourceIds[sourceId - 1]} {onClick} />
+					</div>
+				{/each}
+			</div>
+		</LinkPreview.Content>
+	</LinkPreview.Root>
+{/if}
diff --git a/src/lib/components/chat/Messages/ResponseMessage.svelte b/src/lib/components/chat/Messages/ResponseMessage.svelte
index 98a9dafcc7..2238b21abb 100644
--- a/src/lib/components/chat/Messages/ResponseMessage.svelte
+++ b/src/lib/components/chat/Messages/ResponseMessage.svelte
@@ -797,11 +797,11 @@
 									onTaskClick={async (e) => {
 										console.log(e);
 									}}
-									onSourceClick={async (id, idx) => {
-										console.log(id, idx);
+									onSourceClick={async (id) => {
+										console.log(id);
 
 										if (citationsElement) {
-											citationsElement?.showSourceModal(idx - 1);
+											citationsElement?.showSourceModal(id);
 										}
 									}}
 									onAddMessages={({ modelId, parentId, messages }) => {
diff --git a/src/lib/utils/index.ts b/src/lib/utils/index.ts
index f9fb4236f2..5b92da8b8e 100644
--- a/src/lib/utils/index.ts
+++ b/src/lib/utils/index.ts
@@ -32,7 +32,7 @@ function escapeRegExp(string: string): string {
 	return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
 }
 
-export const replaceTokens = (content, sourceIds, char, user) => {
+export const replaceTokens = (content, char, user) => {
 	const tokens = [
 		{ regex: /{{char}}/gi, replacement: char },
 		{ regex: /{{user}}/gi, replacement: user },
@@ -67,30 +67,6 @@ export const replaceTokens = (content, sourceIds, char, user) => {
 			}
 		});
 
-		if (Array.isArray(sourceIds)) {
-			// Match both [1], [2], and [1,2,3] forms
-			const multiRefRegex = /\[([\d,\s]+)\]/g;
-			segment = segment.replace(multiRefRegex, (match, group) => {
-				// Extract numbers like 1,2,3
-				const indices = group
-					.split(',')
-					.map((n) => parseInt(n.trim(), 10))
-					.filter((n) => !isNaN(n));
-
-				// Replace each index with a <source_id> tag
-				const sources = indices
-					.map((idx) => {
-						const sourceId = sourceIds[idx - 1];
-						return sourceId
-							? `<source_id data="${idx}" title="${encodeURIComponent(sourceId)}" />`
-							: `[${idx}]`;
-					})
-					.join('');
-
-				return sources;
-			});
-		}
-
 		return segment;
 	});
 
diff --git a/src/lib/utils/marked/citation-extension.ts b/src/lib/utils/marked/citation-extension.ts
new file mode 100644
index 0000000000..dad266c9f0
--- /dev/null
+++ b/src/lib/utils/marked/citation-extension.ts
@@ -0,0 +1,55 @@
+export function citationExtension() {
+	return {
+		name: 'citation',
+		level: 'inline' as const,
+
+		start(src: string) {
+			// Trigger on any [number]
+			return src.search(/\[(\d[\d,\s]*)\]/);
+		},
+
+		tokenizer(src: string) {
+			// Avoid matching footnotes
+			if (/^\[\^/.test(src)) return;
+
+			// Match ONE OR MORE adjacent [1] or [1,2] blocks
+			// Example matched: "[1][2,3][4]"
+			const rule = /^(\[(?:\d[\d,\s]*)\])+/;
+			const match = rule.exec(src);
+			if (!match) return;
+
+			const raw = match[0];
+
+			// Extract ALL bracket groups inside the big match
+			const groupRegex = /\[([\d,\s]+)\]/g;
+			const ids: number[] = [];
+			let m: RegExpExecArray | null;
+
+			while ((m = groupRegex.exec(raw))) {
+				const parsed = m[1]
+					.split(',')
+					.map((n) => parseInt(n.trim(), 10))
+					.filter((n) => !isNaN(n));
+
+				ids.push(...parsed);
+			}
+
+			return {
+				type: 'citation',
+				raw,
+				ids // merged list
+			};
+		},
+
+		renderer(token: any) {
+			// e.g. "1,2,3"
+			return token.ids.join(',');
+		}
+	};
+}
+
+export default function () {
+	return {
+		extensions: [citationExtension()]
+	};
+}
diff --git a/src/lib/utils/marked/footnote-extension.ts b/src/lib/utils/marked/footnote-extension.ts
new file mode 100644
index 0000000000..4ef95be6a8
--- /dev/null
+++ b/src/lib/utils/marked/footnote-extension.ts
@@ -0,0 +1,38 @@
+// footnote-extension.ts
+// Simple extension for marked to support footnote references like [^1], [^note]
+
+function escapeHtml(s: string) {
+	return s.replace(
+		/[&<>"']/g,
+		(c) => ({ '&': '&amp;', '<': '&lt;', '>': '&gt;', '"': '&quot;', "'": '&#39;' })[c]!
+	);
+}
+
+export function footnoteExtension() {
+	return {
+		name: 'footnote',
+		level: 'inline' as const,
+		start(src: string) {
+			return src.search(/\[\^\s*[a-zA-Z0-9_-]+\s*\]/);
+		},
+		tokenizer(src: string) {
+			const rule = /^\[\^\s*([a-zA-Z0-9_-]+)\s*\]/;
+			const match = rule.exec(src);
+			if (match) {
+				const escapedText = escapeHtml(match[1]);
+				return {
+					type: 'footnote',
+					raw: match[0],
+					text: match[1],
+					escapedText: escapedText
+				};
+			}
+		}
+	};
+}
+
+export default function () {
+	return {
+		extensions: [footnoteExtension()]
+	};
+}