diff --git a/openneuro/download.py b/openneuro/download.py
index 34fd4f1..4e8c9d4 100644
--- a/openneuro/download.py
+++ b/openneuro/download.py
@@ -4,7 +4,7 @@
 from difflib import get_close_matches
 import hashlib
 import asyncio
-from pathlib import Path
+from pathlib import Path, PosixPath
 import string
 import json
 from typing import Optional, Union
@@ -544,7 +544,8 @@ def _iterate_filenames(
     dataset_id: str,
     tag: str,
     max_retries: int,
-    root: str = ''
+    root: str = '',
+    include: Iterable[str] = tuple(),
 ) -> Generator[dict, None, None]:
     """Iterate over all files in a dataset, yielding filenames."""
     directories = list()
@@ -557,6 +558,37 @@ def _iterate_filenames(
             yield entity
 
     for directory in directories:
+        # Only bother with directories that are in the include list
+        if include:
+            # Take the example:
+            #
+            # --include="sub-CON001/*.eeg"
+            #
+            # or
+            #
+            # --include="sub-CON001"
+            #
+            # or
+            #
+            # --include="sub-CON001/*"
+            #
+            # All three of these should traverse `sub-CON001` and its
+            # subdirectories.
+            n_parts = len(PosixPath(root).parts)
+            dir_include = [PosixPath(inc) for inc in include]
+            dir_include = [  # for stuff like sub-CON001/*
+                '/'.join(inc.parts[:n_parts] + ('*',))
+                for inc in dir_include
+                if len(inc.parts) >= n_parts
+            ] + [  # and stuff like sub-CON001/*.eeg
+                '/'.join(inc.parts[:n_parts - 1] + ('*',))
+                for inc in dir_include
+                if len(inc.parts) >= n_parts - 1 and len(inc.parts) > 1
+            ]  # we want to traverse sub-CON001 in both cases
+            matches_include, _ = _match_include_exclude(
+                directory['filename'], include=dir_include, exclude=[])
+            if dir_include and not any(matches_include):
+                continue
         # Query filenames
         this_dir = directory['filename']
         metadata = _get_download_metadata(
@@ -572,11 +604,27 @@ def _iterate_filenames(
             tag=tag,
             max_retries=max_retries,
             root=this_dir,
+            include=include,
         )
         for path in dir_iterator:
             yield path
 
 
+def _match_include_exclude(
+    filename: str,
+    *,
+    include: Iterable[str],
+    exclude: Iterable[str],
+) -> bool:
+    """Check if a filename matches an include or exclude pattern."""
+    matches_keep = [filename.startswith(i) or fnmatch.fnmatch(filename, i)
+                    for i in include]
+    matches_remove = [filename.startswith(e) or
+                      fnmatch.fnmatch(filename, e)
+                      for e in exclude]
+    return matches_keep, matches_remove
+
+
 def download(*,
              dataset: str,
              tag: Optional[str] = None,
@@ -681,7 +729,8 @@ def download(*,
 
     for file in tqdm(
         _iterate_filenames(
-            these_files, dataset_id=dataset, tag=tag, max_retries=max_retries
+            these_files, dataset_id=dataset, tag=tag, max_retries=max_retries,
+            include=include,
         ),
         desc=_unicode(
             f'Traversing directories for {dataset}', end='', emoji='📁'
@@ -703,12 +752,9 @@ def download(*,
                 include_counts[include.index(filename)] += 1
             continue
 
-        matches_keep = [filename.startswith(i) or fnmatch.fnmatch(filename, i)
-                        for i in include]
-        matches_remove = [filename.startswith(e) or
-                          fnmatch.fnmatch(filename, e)
-                          for e in exclude]
-        if (not include or any(matches_keep)) and not any(matches_remove):
+        matches_keep, matches_exclude = _match_include_exclude(
+            filename, include=include, exclude=exclude)
+        if (not include or any(matches_keep)) and not any(matches_exclude):
             files.append(file)
             # Keep track of include matches.
             if any(matches_keep):
@@ -727,7 +773,7 @@ def download(*,
                 else:
                     extra = (
                         'There were no similar filenames found in the '
-                        'metadata.'
+                        'metadata. '
                     )
                 raise RuntimeError(
                     f'Could not find path in the dataset:\n- {this}\n{extra}'
diff --git a/openneuro/tests/test_download.py b/openneuro/tests/test_download.py
index 259a29d..3d2e7ee 100644
--- a/openneuro/tests/test_download.py
+++ b/openneuro/tests/test_download.py
@@ -8,23 +8,27 @@
 dataset_id_aws = 'ds000246'
 tag_aws = '1.0.0'
 include_aws = 'sub-0001/anat'
+exclude_aws = []
 
 dataset_id_on = 'ds000117'
+tag_on = None
 include_on = 'sub-16/ses-meg'
+exclude_on = '*.fif'  # save GBs of downloads
 
 invalid_tag = 'abcdefg'
 
 
 @pytest.mark.parametrize(
-    ('dataset_id', 'tag', 'include'),
+    ('dataset_id', 'tag', 'include', 'exclude'),
     [
-        (dataset_id_aws, tag_aws, include_aws),
-        (dataset_id_on, None, include_on)
+        (dataset_id_aws, tag_aws, include_aws, exclude_aws),
+        (dataset_id_on, tag_on, include_on, exclude_on),
     ]
 )
-def test_download(tmp_path: Path, dataset_id, tag, include):
+def test_download(tmp_path: Path, dataset_id, tag, include, exclude):
     """Test downloading some files."""
-    download(dataset=dataset_id, tag=tag, target_dir=tmp_path, include=include)
+    download(dataset=dataset_id, tag=tag, target_dir=tmp_path, include=include,
+             exclude=exclude)
 
 
 def test_download_invalid_tag(tmp_path: Path, dataset_id=dataset_id_aws,
@@ -49,14 +53,16 @@ def test_resume_download(tmp_path: Path):
 
     # Download from a different revision / tag
     new_tag = '00001'
+    include = ['CHANGES']
     with pytest.raises(FileExistsError, match=f'revision {tag} exists'):
-        download(dataset=dataset, tag=new_tag, target_dir=tmp_path)
+        download(dataset=dataset, tag=new_tag, target_dir=tmp_path,
+                 include=include)
 
     # Try to "resume" from a different dataset
     new_dataset = 'ds000117'
     with pytest.raises(RuntimeError,
                        match='existing dataset.*appears to be different'):
-        download(dataset=new_dataset, target_dir=tmp_path)
+        download(dataset=new_dataset, target_dir=tmp_path, include=include)
 
     # Remove "DatasetDOI" from JSON
     json_path = tmp_path / 'dataset_description.json'
@@ -100,15 +106,21 @@ def test_doi_handling(tmp_path: Path):
 
     # Now inject a `doi:` prefix into the DOI
     dataset_description_path = tmp_path / 'dataset_description.json'
-    dataset_description = json.loads(
+    dataset_description_text = \
         dataset_description_path.read_text(encoding='utf-8')
-    )
+    dataset_description = json.loads(dataset_description_text)
+    # Make sure we can dumps to get the same thing back (if they change their
+    # indent 4->8 for example, we might try to resume our download of the file
+    # and things will break in a challenging way)
+    dataset_description_rt = json.dumps(dataset_description, indent=4)
+    assert dataset_description_text == dataset_description_rt
+    # Ensure the dataset doesn't already have the problematic prefix, then add
     assert not dataset_description['DatasetDOI'].startswith('doi:')
     dataset_description['DatasetDOI'] = (
         'doi:' + dataset_description['DatasetDOI']
     )
     dataset_description_path.write_text(
-        data=json.dumps(dataset_description, indent=2),
+        data=json.dumps(dataset_description, indent=4),
         encoding='utf-8'
     )
 
diff --git a/pyproject.toml b/pyproject.toml
index 90c796a..542251a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,3 +46,6 @@ build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 # can be left blank
+
+[tool.pytest.ini_options]
+addopts = "-ra -vv --tb=short --durations=10"