diff --git a/src/js/compare/engine/compare-content.ts b/src/js/compare/engine/compare-content.ts
index 2bd8155..64d9209 100644
--- a/src/js/compare/engine/compare-content.ts
+++ b/src/js/compare/engine/compare-content.ts
@@ -41,8 +41,16 @@ export function diffAnnotations(
   baseId: number
 ): CompareTextChange[] {
   const changes: CompareTextChange[] = [];
-  const beforeMap = new Map(before.map((a) => [annotationKey(a), a]));
-  const afterMap = new Map(after.map((a) => [annotationKey(a), a]));
+  const beforeMap = new Map(
+    before
+      .filter(shouldCompareAnnotation)
+      .map((annotation) => [annotationKey(annotation), annotation])
+  );
+  const afterMap = new Map(
+    after
+      .filter(shouldCompareAnnotation)
+      .map((annotation) => [annotationKey(annotation), annotation])
+  );
 
   let idx = baseId;
   for (const [key, ann] of beforeMap) {
@@ -51,8 +59,7 @@ export function diffAnnotations(
         id: `annotation-removed-${idx++}`,
         type: 'removed',
         category: 'annotation',
-        description:
-          `Removed ${ann.subtype} annotation: "${ann.contents || ann.title || ''}"`.trim(),
+        description: formatAnnotationDescription('Removed', ann),
         beforeText: ann.contents || ann.title || '',
         afterText: '',
         beforeRects: [ann.rect],
@@ -67,8 +74,7 @@ export function diffAnnotations(
         id: `annotation-added-${idx++}`,
         type: 'added',
         category: 'annotation',
-        description:
-          `Added ${ann.subtype} annotation: "${ann.contents || ann.title || ''}"`.trim(),
+        description: formatAnnotationDescription('Added', ann),
         beforeText: '',
         afterText: ann.contents || ann.title || '',
         beforeRects: [],
@@ -80,6 +86,26 @@ export function diffAnnotations(
   return changes;
 }
 
+function shouldCompareAnnotation(annotation: CompareAnnotation): boolean {
+  if (annotation.subtype !== 'Highlight') {
+    return true;
+  }
+
+  return Boolean(annotation.contents || annotation.title);
+}
+
+function formatAnnotationDescription(
+  action: 'Added' | 'Removed',
+  annotation: CompareAnnotation
+): string {
+  const label = annotation.contents || annotation.title;
+  if (!label) {
+    return `${action} ${annotation.subtype} annotation`;
+  }
+
+  return `${action} ${annotation.subtype} annotation: "${label}"`;
+}
+
 function annotationKey(ann: CompareAnnotation): string {
   return `${ann.subtype}|${ann.contents}|${Math.round(ann.rect.x)},${Math.round(ann.rect.y)}`;
 }
diff --git a/src/tests/compare/diff-text-runs.test.ts b/src/tests/compare/diff-text-runs.test.ts
index 1ab723e..7e51412 100644
--- a/src/tests/compare/diff-text-runs.test.ts
+++ b/src/tests/compare/diff-text-runs.test.ts
@@ -7,6 +7,7 @@ import {
   sortCompareTextItems,
 } from '@/js/compare/engine/extract-page-model.ts';
 import type {
+  CompareAnnotation,
   ComparePageModel,
   CompareTextItem,
   CompareWordToken,
@@ -23,7 +24,8 @@ function makeItem(id: string, text: string): CompareTextItem {
 
 function makePage(
   pageNumber: number,
-  textItems: CompareTextItem[]
+  textItems: CompareTextItem[],
+  overrides: Partial<ComparePageModel> = {}
 ): ComparePageModel {
   return {
     pageNumber,
@@ -33,6 +35,22 @@ function makePage(
     plainText: textItems.map((item) => item.normalizedText).join(' '),
     hasText: textItems.length > 0,
     source: 'pdfjs',
+    ...overrides,
+  };
+}
+
+function makeAnnotation(
+  subtype: string,
+  overrides: Partial<CompareAnnotation> = {}
+): CompareAnnotation {
+  return {
+    id: `${subtype}-1`,
+    subtype,
+    rect: { x: 0, y: 0, width: 10, height: 10 },
+    contents: '',
+    title: '',
+    color: '',
+    ...overrides,
   };
 }
 
@@ -137,6 +155,25 @@ describe('comparePageModels', () => {
     expect(result.summary.removed).toBe(1);
     expect(result.changes[0].type).toBe('page-removed');
   });
+
+  it('ignores empty highlight annotations in annotation diff output', () => {
+    const result = comparePageModels(
+      makePage(1, [makeItem('a', 'Original')], {
+        annotations: [makeAnnotation('Highlight')],
+      }),
+      makePage(1, [makeItem('b', 'Updated')], {
+        annotations: [makeAnnotation('Highlight', { id: 'highlight-2' })],
+      })
+    );
+
+    expect(
+      result.changes.some(
+        (change) =>
+          change.category === 'annotation' &&
+          change.description.includes('Highlight annotation')
+      )
+    ).toBe(false);
+  });
 });
 
 describe('sortCompareTextItems', () => {