diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py
index f93c2217419..e9fcbf2c4dd 100644
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -83,6 +83,7 @@ class Configuration( object ):
         # The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution
         # and moved to the tool shed.
         self.integrated_tool_panel_config = resolve_path( kwargs.get( 'integrated_tool_panel_config', 'integrated_tool_panel.xml' ), self.root )
+        self.toolbox_filter_base_modules = listify( kwargs.get( "toolbox_filter_base_modules", "galaxy.tools.filters" ) )
         self.tool_filters = listify( kwargs.get( "tool_filters", [] ), do_strip=True )
         self.tool_label_filters = listify( kwargs.get( "tool_label_filters", [] ), do_strip=True )
         self.tool_section_filters = listify( kwargs.get( "tool_section_filters", [] ), do_strip=True )
diff --git a/lib/galaxy/tools/filters/__init__.py b/lib/galaxy/tools/filters/__init__.py
index 04d72ff1e38..c7402d176f0 100644
--- a/lib/galaxy/tools/filters/__init__.py
+++ b/lib/galaxy/tools/filters/__init__.py
@@ -1,6 +1,8 @@
-import logging
-from galaxy.util import listify
 from copy import deepcopy
+import sys
+import logging
+
+from galaxy.util import listify
 
 log = logging.getLogger( __name__ )
 
@@ -20,6 +22,7 @@ class FilterFactory( object ):
         self.default_filters = dict( tool=[ _not_hidden, _handle_requires_login ], section=[], label=[] )
         # Add dynamic filters to these default filters.
         config = toolbox.app.config
+        self.__base_modules = listify( getattr( config, "toolbox_filter_base_modules", "galaxy.tools.filters" ) )
         self.__init_filters( "tool", getattr( config, "tool_filters", "" ), self.default_filters )
         self.__init_filters( "section", getattr( config, "tool_section_filters", "" ), self.default_filters )
         self.__init_filters( "label", getattr( config, "tool_label_filters", "" ), self.default_filters )
@@ -65,14 +68,27 @@ class FilterFactory( object ):
         if ":" in filter_name:
             # Should be a submodule of filters (e.g. examples:restrict_development_tools)
             (module_name, function_name) = filter_name.rsplit(":", 1)
-            module = __import__( module_name.strip(), globals() )
-            function = getattr( module, function_name.strip() )
+            function = self._import_filter( module_name, function_name )
         else:
             # No module found, just load a function from this file or
             # one that has be explicitly imported.
             function = getattr( globals(), filter_name.strip() )
         return function
 
+    def _import_filter( self, module_name, function_name ):
+        function_name = function_name.strip()
+        for base_module in self.__base_modules:
+            full_module_name = "%s.%s" % ( base_module, module_name.strip() )
+            try:
+                __import__( full_module_name )
+            except ImportError:
+                # log.debug("Failed to load module.", exc_info=True)
+                continue
+            module = sys.modules[ full_module_name ]
+            if hasattr( module, function_name ):
+                return getattr( module, function_name )
+        raise Exception("Failed to find filter %s.%s" % (module_name, function_name))
+
 
 ## Stock Filter Functions
 def _not_hidden( context, tool ):
diff --git a/test/unit/tools/filter_modules/__init__.py b/test/unit/tools/filter_modules/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/unit/tools/filter_modules/filtermod.py b/test/unit/tools/filter_modules/filtermod.py
new file mode 100644
index 00000000000..64adfd451b0
--- /dev/null
+++ b/test/unit/tools/filter_modules/filtermod.py
@@ -0,0 +1,22 @@
+""" Test filters used by test_toolbox_filters.py.
+"""
+
+
+def filter_tool( context, tool ):
+    """Test Filter Tool"""
+    return False
+
+
+def filter_section( context, section ):
+    """Test Filter Section"""
+    return False
+
+
+def filter_label_1( context, label ):
+    """Test Filter Label 1"""
+    return False
+
+
+def filter_label_2( context, label ):
+    """Test Filter Label 2"""
+    return False
diff --git a/test/unit/tools/test_toolbox_filters.py b/test/unit/tools/test_toolbox_filters.py
new file mode 100644
index 00000000000..482b59d91f0
--- /dev/null
+++ b/test/unit/tools/test_toolbox_filters.py
@@ -0,0 +1,79 @@
+from galaxy.util.bunch import Bunch
+
+from galaxy.tools.filters import FilterFactory
+
+
+def test_stock_filtering_requires_login_tools( ):
+    anonymous_user_trans = mock_trans( has_user=False )
+    filters = filter_factory( {} ).build_filters( mock_trans() )[ 'tool' ]
+    assert not is_filtered( filters, anonymous_user_trans, mock_tool( require_login=False ) )
+    assert is_filtered( filters, anonymous_user_trans, mock_tool( require_login=True ) )
+
+    logged_in_trans = mock_trans( has_user=True )
+    filters = filter_factory( {} ).build_filters( logged_in_trans )[ 'tool' ]
+    assert not is_filtered( filters, logged_in_trans, mock_tool( require_login=True ) )
+
+
+def test_stock_filtering_hidden_tools( ):
+    filters = filter_factory( {} ).build_filters( mock_trans() )[ 'tool' ]
+    assert not is_filtered( filters, mock_trans(), mock_tool( hidden=False ) )
+    assert is_filtered( filters, mock_trans(), mock_tool( hidden=True ) )
+
+
+def test_trackster_filtering( ):
+    filters = filter_factory( {} ).build_filters( mock_trans(), trackster=True )[ 'tool' ]
+    # Ekkk... is trackster_conf broken? Why is it showing up.
+    # assert is_filtered( filters, mock_trans(), mock_tool( trackster_conf=False ) )
+    assert not is_filtered( filters, mock_trans(), mock_tool( trackster_conf=True ) )
+
+
+def test_custom_filters():
+    filters = filter_factory().build_filters( mock_trans() )
+    tool_filters = filters[ "tool" ]
+    # TODO: the fact that -1 is the custom filter is an implementation
+    # detail that should not be tested here.
+    assert tool_filters[ -1 ].__doc__ == "Test Filter Tool"
+
+    section_filters = filters[ "section" ]
+    assert section_filters[ 0 ].__doc__ == "Test Filter Section"
+
+    label_filters = filters[ "label" ]
+    assert label_filters[ 0 ].__doc__ == "Test Filter Label 1"
+    assert label_filters[ 1 ].__doc__ == "Test Filter Label 2"
+
+
+def filter_factory(config_dict=None):
+    if config_dict is None:
+        config_dict = dict(
+            tool_filters=["filtermod:filter_tool"],
+            tool_section_filters=["filtermod:filter_section"],
+            tool_label_filters=["filtermod:filter_label_1", "filtermod:filter_label_2"],
+        )
+    config = Bunch( **config_dict )
+    config.toolbox_filter_base_modules = "galaxy.tools.filters,tools.filter_modules"
+    app = Bunch(config=config)
+    toolbox = Bunch(app=app)
+    return FilterFactory(toolbox)
+
+
+def is_filtered( filters, trans, tool ):
+    context = Bunch( trans=trans )
+    return not all( map( lambda filter: filter( context, tool ), filters ) )
+
+
+def mock_tool( require_login=False, hidden=False, trackster_conf=False ):
+    tool = Bunch(
+        require_login=require_login,
+        hidden=hidden,
+        trackster_conf=trackster_conf,
+    )
+    return tool
+
+
+def mock_trans( has_user=True ):
+    trans = Bunch( )
+    if has_user:
+        trans.user = Bunch(preferences={})
+    else:
+        trans.user = None
+    return trans