diff --git a/doc/usage.rst b/doc/usage.rst
index 5a94d9e..841924c 100644
--- a/doc/usage.rst
+++ b/doc/usage.rst
@@ -145,6 +145,9 @@ data files based on the given version string. The remote URL will also be update
 Notice that there is a format specifier ``{version}`` in the URL that Pooch substitutes
 for you.
 
+Versioning is optional and can be ignored by omitting the ``version`` and
+``version_dev`` arguments or setting them to ``None``.
+
 
 User-defined paths
 -------------------
@@ -245,3 +248,66 @@ fictitious project from the command-line:
 .. code:: bash
 
    $ python -c "import pooch; pooch.make_registry('data', 'plumbus/registry.txt')"
+
+
+Multiple URLs
+-------------
+
+You can set a custom download URL for individual files with the ``urls`` argument of
+:func:`pooch.create` or :class:`pooch.Pooch`. It should be a dictionary with the file
+names as keys and the URLs for downloading the files as values. For example, say we have
+a ``citadel.csv`` file that we want to download from
+``https://www.some-data-hosting-site.com`` instead:
+
+.. code:: python
+
+    # The basic setup is the same and we must include citadel.csv in the registry.
+    GOODBOY = pooch.create(
+        path=pooch.os_cache("plumbus"),
+        base_url="https://github.com/rick/plumbus/raw/{version}/data/",
+        version=version,
+        version_dev="master",
+        registry={
+            "c137.csv": "19uheidhlkjdwhoiwuhc0uhcwljchw9ochwochw89dcgw9dcgwc",
+            "cronen.csv": "1upodh2ioduhw9celdjhlfvhksgdwikdgcowjhcwoduchowjg8w",
+            "citadel.csv": "893yprofwjndcwhx9c0ehp3ue9gcwoscjwdfgh923e0hwhcwiyc",
+        },
+        # Now specify custom URLs for some of the files in the registry.
+        urls={
+            "citadel.csv": "https://www.some-data-hosting-site.com/files/citadel.csv",
+        },
+    )
+
+Notice that versioning of custom URLs is not supported (since they are assumed to be
+data files independent of your project) and the file name will not be appended
+automatically to the URL (in case you want to change the file name in local storage).
+
+Custom URLs can be used along side ``base_url`` or you can omit ``base_url`` entirely by
+setting it to an empty string (``base_url=""``). However, doing so requires setting a
+custom URL for every file in the registry.
+
+You can also include custom URLs in a registry file by adding the URL for a file to end
+of the line (separated by a space):
+
+.. code-block:: none
+
+    c137.csv 19uheidhlkjdwhoiwuhc0uhcwljchw9ochwochw89dcgw9dcgwc
+    cronen.csv 1upodh2ioduhw9celdjhlfvhksgdwikdgcowjhcwoduchowjg8w
+    citadel.csv 893yprofwjndcwhx9c0ehp3ue9gcwoscjwdfgh923e0hwhcwiyc https://www.some-data-hosting-site.com/files/citadel.csv
+
+:meth:`pooch.Pooch.load_registry` will automatically populate the ``urls`` attribute.
+This way, custom URLs don't need to be set in the code. In fact, the module code doesn't
+change at all:
+
+.. code:: python
+
+    # Define the Pooch exactly the same (urls is None by default)
+    GOODBOY = pooch.create(
+        path=pooch.os_cache("plumbus"),
+        base_url="https://github.com/rick/plumbus/raw/{version}/data/",
+        version=version,
+        version_dev="master",
+        registry=None,
+    )
+    # If custom URLs are present in the registry file, they will be set automatically
+    GOODBOY.load_registry(os.path.join(os.path.dirname(__file__), "registry.txt"))
diff --git a/pooch/core.py b/pooch/core.py
index 5d2c3ef..8a2bc11 100644
--- a/pooch/core.py
+++ b/pooch/core.py
@@ -18,7 +18,15 @@ if sys.version_info[0] < 3:
     PermissionError = OSError  # pylint: disable=redefined-builtin,invalid-name
 
 
-def create(path, base_url, version=None, version_dev="master", env=None, registry=None):
+def create(
+    path,
+    base_url,
+    version=None,
+    version_dev="master",
+    env=None,
+    registry=None,
+    urls=None,
+):
     """
     Create a new :class:`~pooch.Pooch` with sensible defaults to fetch data files.
 
@@ -55,11 +63,16 @@ def create(path, base_url, version=None, version_dev="master", env=None, registr
         An environment variable that can be used to overwrite *path*. This allows users
         to control where they want the data to be stored. We'll append *version* to the
         end of this value as well.
-    registry : dict
+    registry : dict or None
         A record of the files that are managed by this Pooch. Keys should be the file
         names and the values should be their SHA256 hashes. Only files in the registry
         can be fetched from the local storage. Files in subdirectories of *path* **must
         use Unix-style separators** (``'/'``) even on Windows.
+    urls : dict or None
+        Custom URLs for downloading individual files in the registry. A dictionary with
+        the file names as keys and the custom URLs as values. Not all files in
+        *registry* need an entry in *urls*. If a file has an entry in *urls*, the
+        *base_url* will be ignored when downloading it in favor of ``urls[fname]``.
 
 
     Returns
@@ -160,9 +173,7 @@ def create(path, base_url, version=None, version_dev="master", env=None, registr
                 )
             )
         warn(message)
-    if registry is None:
-        registry = dict()
-    pup = Pooch(path=Path(path), base_url=base_url, registry=registry)
+    pup = Pooch(path=Path(path), base_url=base_url, registry=registry, urls=urls)
     return pup
 
 
@@ -178,18 +189,28 @@ class Pooch:
     base_url : str
         Base URL for the remote data source. All requests will be made relative to this
         URL.
-    registry : dict
+    registry : dict or None
         A record of the files that are managed by this good boy. Keys should be the file
         names and the values should be their SHA256 hashes. Only files in the registry
         can be fetched from the local storage. Files in subdirectories of *path* **must
         use Unix-style separators** (``'/'``) even on Windows.
+    urls : dict or None
+        Custom URLs for downloading individual files in the registry. A dictionary with
+        the file names as keys and the custom URLs as values. Not all files in
+        *registry* need an entry in *urls*. If a file has an entry in *urls*, the
+        *base_url* will be ignored when downloading it in favor of ``urls[fname]``.
 
     """
 
-    def __init__(self, path, base_url, registry):
+    def __init__(self, path, base_url, registry=None, urls=None):
         self.path = path
         self.base_url = base_url
+        if registry is None:
+            registry = dict()
         self.registry = dict(registry)
+        if urls is None:
+            urls = dict()
+        self.urls = dict(urls)
 
     @property
     def abspath(self):
@@ -245,6 +266,8 @@ class Pooch:
         """
         Download a file from the remote data storage to the local storage.
 
+        Used by :meth:`~pooch.Pooch.fetch` to do the actual downloading.
+
         Parameters
         ----------
         fname : str
@@ -258,7 +281,7 @@ class Pooch:
 
         """
         destination = self.abspath / fname
-        source = "".join([self.base_url, fname])
+        source = self.urls.get(fname, "".join([self.base_url, fname]))
         # Stream the file to a temporary so that we can safely check its hash before
         # overwriting the original
         with tempfile.NamedTemporaryFile(delete=False) as fout:
@@ -288,7 +311,8 @@ class Pooch:
         Use this if you are managing many files.
 
         Each line of the file should have file name and its SHA256 hash separate by a
-        space. Only one file per line is allowed.
+        space. Only one file per line is allowed. Custom download URLs for individual
+        files can be specified as a third element on the line.
 
         Parameters
         ----------
@@ -299,11 +323,15 @@ class Pooch:
         with open(fname) as fin:
             for linenum, line in enumerate(fin):
                 elements = line.strip().split()
-                if len(elements) != 2:
-                    raise ValueError(
-                        "Expected 2 elements in line {} but got {}.".format(
+                if len(elements) > 3 or len(elements) < 2:
+                    raise IOError(
+                        "Expected 2 or 3 elements in line {} but got {}.".format(
                             linenum, len(elements)
                         )
                     )
-                file_name, file_sha256 = elements
+                file_name = elements[0]
+                file_sha256 = elements[1]
+                if len(elements) == 3:
+                    file_url = elements[2]
+                    self.urls[file_name] = file_url
                 self.registry[file_name] = file_sha256

diff --git a/pooch/tests/data/registry-custom-url.txt b/pooch/tests/data/registry-custom-url.txt
new file mode 100644
index 0000000..d49b0eb
--- /dev/null
+++ b/pooch/tests/data/registry-custom-url.txt
@@ -0,0 +1,2 @@
+subdir/tiny-data.txt baee0894dba14b12085eacb204284b97e362f4f3e5a5807693cc90ef415c1b2d
+tiny-data.txt baee0894dba14b12085eacb204284b97e362f4f3e5a5807693cc90ef415c1b2d https://some-site/tiny-data.txt
diff --git a/pooch/tests/data/registry-invalid.txt b/pooch/tests/data/registry-invalid.txt
index 69c9cd9..0447a4e 100644
--- a/pooch/tests/data/registry-invalid.txt
+++ b/pooch/tests/data/registry-invalid.txt
@@ -1,2 +1,2 @@
 tiny-data.txt baee0894dba14b12085eacb204284b97e362f4f3e5a5807693cc90ef415c1b2d
-some-file.txt second_element third_element
+some-file.txt second_element third_element forth_element
diff --git a/pooch/tests/test_core.py b/pooch/tests/test_core.py
index 28d6bb0..41eccec 100644
--- a/pooch/tests/test_core.py
+++ b/pooch/tests/test_core.py
@@ -42,6 +42,23 @@ def test_pooch_local():
     check_tiny_data(fname)
 
 
+def test_pooch_custom_url():
+    "Have pooch download the file from URL that is not base_url"
+    with TemporaryDirectory() as local_store:
+        path = Path(local_store)
+        urls = {"tiny-data.txt": BASEURL + "tiny-data.txt"}
+        # Setup a pooch in a temp dir
+        pup = Pooch(path=path, base_url="", registry=REGISTRY, urls=urls)
+        # Check that the warning says that the file is being updated
+        with warnings.catch_warnings(record=True) as warn:
+            fname = pup.fetch("tiny-data.txt")
+            assert len(warn) == 1
+            assert issubclass(warn[-1].category, UserWarning)
+            assert str(warn[-1].message).split()[0] == "Downloading"
+            assert str(warn[-1].message).split()[-1] == "'{}'.".format(path)
+        check_tiny_data(fname)
+
+
 def test_pooch_update():
     "Setup a pooch that already has the local data but the file is outdated"
     with TemporaryDirectory() as local_store:
@@ -101,15 +118,23 @@ def test_pooch_file_not_in_registry():
 
 def test_pooch_load_registry():
     "Loading the registry from a file should work"
-    pup = Pooch(path="", base_url="", registry={})
+    pup = Pooch(path="", base_url="")
     pup.load_registry(os.path.join(DATA_DIR, "registry.txt"))
     assert pup.registry == REGISTRY
 
 
+def test_pooch_load_registry_custom_url():
+    "Load the registry from a file with a custom URL inserted"
+    pup = Pooch(path="", base_url="")
+    pup.load_registry(os.path.join(DATA_DIR, "registry-custom-url.txt"))
+    assert pup.registry == REGISTRY
+    assert pup.urls == {"tiny-data.txt": "https://some-site/tiny-data.txt"}
+
+
 def test_pooch_load_registry_invalid_line():
     "Should raise an exception when a line doesn't have two elements"
     pup = Pooch(path="", base_url="", registry={})
-    with pytest.raises(ValueError):
+    with pytest.raises(IOError):
         pup.load_registry(os.path.join(DATA_DIR, "registry-invalid.txt"))
 
 

Data in more than one remote source
Right now, we assume that all the sample data is in the same remote source. This might not be the case for many projects if they are using publicly available data. It would be great to be able to specify the a remote URL for individual entries in the registry (which should probably not be versioned). 

One of doing this that might not require much refactoring is to include a new attribute in `Pooch.registry_urls` that is a dictionary mapping file names to remote URLs where they can be downloaded.  We should not append the file name to this URL. The `Pooch._download_file` method can then check `if fname in self.registry_urls` and use `self.registry_urls[fname]` as the download source instead.
pooch/tests/test_core.py::test_pooch_load_registry pooch/tests/test_core.py::test_pooch_load_registry_custom_url pooch/tests/test_core.py::test_pooch_load_registry_invalid_line
pooch/tests/test_core.py::test_pooch_local pooch/tests/test_core.py::test_pooch_file_not_in_registry pooch/tests/test_core.py::test_create_makedirs_permissionerror pooch/tests/test_core.py::test_create_newfile_permissionerror