diff --git a/src/NwcIO/Model/Diff/NwcDiffEngine.cs b/src/NwcIO/Model/Diff/NwcDiffEngine.cs
index 519451c..c84a82c 100644
--- a/src/NwcIO/Model/Diff/NwcDiffEngine.cs
+++ b/src/NwcIO/Model/Diff/NwcDiffEngine.cs
@@ -68,19 +68,21 @@ private static void PerformDiff(
         List<DiffItem> revItems,
         NwcDiffOptions options)
     {
-        // 1. Build lookup tables: by Guid first, then by composite MatchKey
-        var baseByGuid = new Dictionary<Guid, DiffItem>();
-        var baseByKey = new Dictionary<string, DiffItem>(StringComparer.OrdinalIgnoreCase);
+        // 1. Build lookup tables: by Guid first, then by composite MatchKey. Several baseline items can share a GUID
+        // (or, across the models of an assembly, a key), so each entry queues them in order and a match takes the
+        // first one: every baseline item is matched at most once.
+        var baseByGuid = new Dictionary<Guid, Queue<DiffItem>>();
+        var baseByKey = new Dictionary<string, Queue<DiffItem>>(StringComparer.OrdinalIgnoreCase);
 
         foreach (var item in baseItems)
         {
             if (item.ElementGuid.HasValue && item.ElementGuid.Value != Guid.Empty)
             {
-                baseByGuid[item.ElementGuid.Value] = item;
+                Enqueue(baseByGuid, item.ElementGuid.Value, item);
             }
             else
             {
-                baseByKey[item.MatchKey] = item;
+                Enqueue(baseByKey, item.MatchKey, item);
             }
         }
 
@@ -97,11 +99,11 @@ private static void PerformDiff(
             DiffItem? baseItem = null;
             if (rev.ElementGuid.HasValue && rev.ElementGuid.Value != Guid.Empty)
             {
-                baseByGuid.TryGetValue(rev.ElementGuid.Value, out baseItem);
+                baseItem = Dequeue(baseByGuid, rev.ElementGuid.Value);
             }
             if (baseItem is null && !string.IsNullOrEmpty(rev.MatchKey))
             {
-                baseByKey.TryGetValue(rev.MatchKey, out baseItem);
+                baseItem = Dequeue(baseByKey, rev.MatchKey);
             }
 
             if (baseItem is null)
@@ -221,6 +223,22 @@ private static void PerformDiff(
         }
     }
 
+    private static void Enqueue<TKey>(Dictionary<TKey, Queue<DiffItem>> lookup, TKey key, DiffItem item)
+        where TKey : notnull
+    {
+        if (!lookup.TryGetValue(key, out var queue))
+        {
+            queue = new Queue<DiffItem>();
+            lookup[key] = queue;
+        }
+
+        queue.Enqueue(item);
+    }
+
+    private static DiffItem? Dequeue<TKey>(Dictionary<TKey, Queue<DiffItem>> lookup, TKey key)
+        where TKey : notnull =>
+        lookup.TryGetValue(key, out var queue) && queue.TryDequeue(out var item) ? item : null;
+
     private static bool PassesFilter(DiffItem item, string? filter)
     {
         if (string.IsNullOrWhiteSpace(filter)) return true;
diff --git a/tests/NwcIO.Tests/DiffEngineTests.cs b/tests/NwcIO.Tests/DiffEngineTests.cs
index d576a85..10c6c3d 100644
--- a/tests/NwcIO.Tests/DiffEngineTests.cs
+++ b/tests/NwcIO.Tests/DiffEngineTests.cs
@@ -244,4 +244,72 @@ public void FederatedAssembly_CompareProducesReport()
         Assert.Equal("MeshNew", report.Added[0].Name);
         Assert.Single(report.Unchanged);
     }
+
+    private static NwcDocument CreateSharedGuidDocument(Guid guid, int count)
+    {
+        var root = new NwcNode { Id = 1, Name = "Root", Class = "Root" };
+        for (int i = 0; i < count; i++)
+        {
+            root.Children.Add(new NwcNode { Id = 2 + i, Name = "Part", Class = "LcRevitData_Element", ElementGuid = guid });
+        }
+
+        return NwcDocument.Create(rootNode: root);
+    }
+
+    [Fact]
+    public void Compare_DuplicateGuidsInDocument_MatchesEachElementOnce()
+    {
+        var guid = Guid.NewGuid();
+
+        var report = CreateSharedGuidDocument(guid, 3).Compare(CreateSharedGuidDocument(guid, 3));
+
+        Assert.Empty(report.Added);
+        Assert.Empty(report.Deleted);
+        Assert.Empty(report.Modified);
+        Assert.Equal(3, report.Unchanged.Count);
+        Assert.Equal([2, 3, 4], report.Unchanged.Select(d => d.BaselineNode!.Id).Order());
+    }
+
+    [Fact]
+    public void Compare_DuplicateGuidRemovedFromRevision_ReportsOneDeletion()
+    {
+        var guid = Guid.NewGuid();
+
+        var report = CreateSharedGuidDocument(guid, 3).Compare(CreateSharedGuidDocument(guid, 2));
+
+        Assert.Empty(report.Added);
+        Assert.Single(report.Deleted);
+        Assert.Equal(2, report.Unchanged.Count);
+    }
+
+    [Fact]
+    public void Compare_GuidSharedAcrossAssemblyModels_MatchesEachElementOnce()
+    {
+        var guid = Guid.NewGuid();
+        var baseline = NwcAssembly.Create("A", CreateSharedGuidDocument(guid, 1), CreateSharedGuidDocument(guid, 1));
+        var revision = NwcAssembly.Create("B", CreateSharedGuidDocument(guid, 1), CreateSharedGuidDocument(guid, 1));
+
+        var report = baseline.Compare(revision);
+
+        Assert.Empty(report.Added);
+        Assert.Empty(report.Deleted);
+        Assert.Equal(2, report.Unchanged.Count);
+    }
+
+    [Fact]
+    public void Compare_SameMeshNameAcrossAssemblyModels_MatchesEachElementOnce()
+    {
+        var baseline = NwcAssembly.Create("A",
+            NwcDocument.Create(meshes: [CreateBoxMesh(1, "Wall", new Vector3d(0, 0, 0))]),
+            NwcDocument.Create(meshes: [CreateBoxMesh(1, "Wall", new Vector3d(0, 0, 0))]));
+        var revision = NwcAssembly.Create("B",
+            NwcDocument.Create(meshes: [CreateBoxMesh(1, "Wall", new Vector3d(0, 0, 0))]),
+            NwcDocument.Create(meshes: [CreateBoxMesh(1, "Wall", new Vector3d(0, 0, 0))]));
+
+        var report = baseline.Compare(revision);
+
+        Assert.Empty(report.Added);
+        Assert.Empty(report.Deleted);
+        Assert.Equal(2, report.Unchanged.Count);
+    }
 }