diff --git a/tests/cases/csv_points_source.py b/tests/cases/csv_points_source.py
index 1fec0833..66ba613a 100644
--- a/tests/cases/csv_points_source.py
+++ b/tests/cases/csv_points_source.py
@@ -2,6 +2,7 @@
 
 import numpy as np
 import pytest
+import csv
 
 from gunpowder import (
     BatchRequest,
@@ -22,7 +23,7 @@ def seeds():
 
 
 @pytest.fixture
-def test_points(tmpdir):
+def test_points_2d(tmpdir):
     random.seed(1234)
     np.random.seed(1234)
 
@@ -41,8 +42,31 @@ def test_points(tmpdir):
     yield fake_points_file, fake_points
 
 
-def test_pipeline3(test_points):
-    fake_points_file, fake_points = test_points
+@pytest.fixture
+def test_points_3d(tmpdir):
+    random.seed(1234)
+    np.random.seed(1234)
+
+    fake_points_file = tmpdir / "shift_test.csv"
+    fake_points = np.random.randint(0, 100, size=(3, 3)).astype(float)
+    with open(fake_points_file, "w") as f:
+        writer = csv.DictWriter(f, fieldnames=["x", "y", "z", "id"])
+        writer.writeheader()
+        for i, point in enumerate(fake_points):
+            pointdict = {"x": point[0], "y": point[1], "z": point[2], "id": i}
+            writer.writerow(pointdict)
+
+    # This fixture will run after seeds since it is set
+    # with autouse=True. So make sure to reset the seeds properly at the end
+    # of this fixture
+    random.seed(12345)
+    np.random.seed(12345)
+
+    yield fake_points_file, fake_points
+
+
+def test_pipeline_2d(test_points_2d):
+    fake_points_file, fake_points = test_points_2d
 
     points_key = GraphKey("TEST_POINTS")
 
@@ -67,3 +91,35 @@ def test_pipeline3(test_points):
     result_locs = [list(point.location) for point in result_points]
 
     assert sorted(result_locs) == sorted(target_locs)
+
+
+def test_pipeline_3d(test_points_3d):
+    fake_points_file, fake_points = test_points_3d
+
+    points_key = GraphKey("TEST_POINTS")
+    scale = 2
+    csv_source = CsvPointsSource(
+        fake_points_file,
+        points_key,
+        spatial_cols=[0, 2, 1],
+        delimiter=",",
+        id_col=3,
+        points_spec=GraphSpec(roi=Roi(shape=Coordinate((100, 100)), offset=(0, 0))),
+        scale=scale,
+    )
+
+    request = BatchRequest()
+    shape = Coordinate((100, 100, 100))
+    request.add(points_key, shape)
+
+    pipeline = csv_source
+    with build(pipeline) as b:
+        request = b.request_batch(request)
+
+    result_points = list(request[points_key].nodes)
+    for node in result_points:
+        orig_loc = fake_points[int(node.id)]
+        reordered_loc = orig_loc.copy()
+        reordered_loc[1] = orig_loc[2]
+        reordered_loc[2] = orig_loc[1]
+        assert list(node.location) == list(reordered_loc * scale)