diff --git a/bg_atlasgen/validate_atlases.py b/bg_atlasgen/validate_atlases.py
index b9568bf..6a0d7c6 100644
--- a/bg_atlasgen/validate_atlases.py
+++ b/bg_atlasgen/validate_atlases.py
@@ -110,8 +110,9 @@ def check_additional_references(atlas: BrainGlobeAtlas):
     pass
 
 
-def validate_mesh_structure_pairs(atlas: BrainGlobeAtlas):
-    """Ensure mesh files (.obj) exist for each expected structure in the atlas."""
+def catch_missing_mesh_files(atlas: BrainGlobeAtlas):
+    """Checks if all the structures in the atlas have a corresponding mesh file"""
+
     ids_from_bg_atlas_api = list(atlas.structures.keys())
 
     atlas_path = (
@@ -126,19 +127,41 @@ def validate_mesh_structure_pairs(atlas: BrainGlobeAtlas):
         if file.endswith(".obj")
     ]
 
-    in_mesh_not_bg = []
-    for id in ids_from_mesh_files:
-        if id not in ids_from_bg_atlas_api:
-            in_mesh_not_bg.append(id)
-
     in_bg_not_mesh = []
     for id in ids_from_bg_atlas_api:
         if id not in ids_from_mesh_files:
             in_bg_not_mesh.append(id)
 
-    if len(in_mesh_not_bg) or len(in_bg_not_mesh):
+    if len(in_bg_not_mesh) != 0:
+        raise AssertionError(
+            f"Structures with IDs {in_bg_not_mesh} are in the atlas, but don't have a corresponding mesh file."
+        )
+
+
+def catch_missing_structures(atlas: BrainGlobeAtlas):
+    """Checks if all the mesh files in the atlas folder are listed as a structure in the atlas"""
+
+    ids_from_bg_atlas_api = list(atlas.structures.keys())
+
+    atlas_path = (
+        Path(get_brainglobe_dir())
+        / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+    )
+    obj_path = Path(atlas_path / "meshes")
+
+    ids_from_mesh_files = [
+        int(Path(file).stem)
+        for file in os.listdir(obj_path)
+        if file.endswith(".obj")
+    ]
+
+    in_mesh_not_bg = []
+    for id in ids_from_mesh_files:
+        if id not in ids_from_bg_atlas_api:
+            in_mesh_not_bg.append(id)
+
+    if len(in_mesh_not_bg) != 0:
         raise AssertionError(
-            f"Structures with ID {in_bg_not_mesh} are in the atlas, but don't have a corresponding mesh file; "
             f"Structures with IDs {in_mesh_not_bg} have a mesh file, but are not accessible through the atlas."
         )
 
@@ -176,7 +199,8 @@ def validate_atlas(atlas_name, version, validation_functions):
         open_for_visual_check,
         validate_checksum,
         check_additional_references,
-        validate_mesh_structure_pairs,
+        catch_missing_mesh_files,
+        catch_missing_structures,
     ]
 
     valid_atlases = []
diff --git a/tests/test_unit/test_validation.py b/tests/test_unit/test_validation.py
index 5fcf9f0..bcffe25 100644
--- a/tests/test_unit/test_validation.py
+++ b/tests/test_unit/test_validation.py
@@ -7,6 +7,8 @@
 
 from bg_atlasgen.validate_atlases import (
     _assert_close,
+    catch_missing_mesh_files,
+    catch_missing_structures,
     validate_atlas_files,
     validate_mesh_matches_image_extents,
 )
@@ -34,6 +36,17 @@ def atlas_with_bad_reference_file():
     os.rename(bad_name, good_name)
 
 
+@pytest.fixture
+def atlas_with_missing_structure():
+    atlas = BrainGlobeAtlas("osten_mouse_100um")
+    modified_structures = atlas.structures.copy()
+    modified_structures.pop(688)
+
+    modified_atlas = BrainGlobeAtlas("osten_mouse_100um")
+    modified_atlas.structures = modified_structures
+    return modified_atlas
+
+
 def test_validate_mesh_matches_image_extents(atlas):
     assert validate_mesh_matches_image_extents(atlas)
 
@@ -69,3 +82,38 @@ def test_assert_close_negative():
         AssertionError, match="differ by more than 10 times pixel size"
     ):
         _assert_close(99.5, 30, 2)
+
+
+def test_catch_missing_mesh_files(atlas):
+    """
+    Tests if catch_missing_mesh_files function raises an error,
+    when there is at least one structure in the atlas that doesn't have
+    a corresponding obj file.
+
+    Expected behaviour:
+    True for "allen_mouse_10um" (structure 545 doesn't have an obj file): fails
+    the validation function, raises an error --> no output from this test function
+    """
+
+    with pytest.raises(
+        AssertionError,
+        match=r"Structures with IDs \[.*?\] are in the atlas, but don't have a corresponding mesh file.",
+    ):
+        catch_missing_mesh_files(atlas)
+
+
+def test_catch_missing_structures(atlas_with_missing_structure):
+    """
+    Tests if catch_missing_structures function raises an error,
+    when there is at least one orphan obj file (doesn't have a corresponding structure in the atlas)
+
+    Expected behaviour:
+    Currently no atlas fails the validation function this way so the [] is always empty
+    --> this test function should always raise an error
+    """
+
+    with pytest.raises(
+        AssertionError,
+        match=r"Structures with IDs \[.*?\] have a mesh file, but are not accessible through the atlas.",
+    ):
+        catch_missing_structures(atlas_with_missing_structure)