diff --git a/pcbnew/drc/drc_engine.cpp b/pcbnew/drc/drc_engine.cpp
index 42e216f838..51d7ccc6b0 100644
--- a/pcbnew/drc/drc_engine.cpp
+++ b/pcbnew/drc/drc_engine.cpp
@@ -729,7 +729,7 @@ DRC_CONSTRAINT DRC_ENGINE::EvalRulesForItems( DRC_CONSTRAINT_T aConstraintId,
     bool                  implicit = false;
 
     // Local overrides take precedence
-    if( aConstraintId == CLEARANCE_CONSTRAINT )
+    if( aConstraintId == CLEARANCE_CONSTRAINT || aConstraintId == HOLE_CLEARANCE_CONSTRAINT )
     {
         int overrideA = 0;
         int overrideB = 0;
@@ -756,7 +756,7 @@ DRC_CONSTRAINT DRC_ENGINE::EvalRulesForItems( DRC_CONSTRAINT_T aConstraintId,
 
         if( overrideA || overrideB )
         {
-            DRC_CONSTRAINT constraint( CLEARANCE_CONSTRAINT, m_msg );
+            DRC_CONSTRAINT constraint( aConstraintId, m_msg );
             constraint.m_Value.SetMin( std::max( overrideA, overrideB ) );
             return constraint;
         }
diff --git a/pcbnew/drc/drc_rtree.h b/pcbnew/drc/drc_rtree.h
index faf7e21f65..c0e5bdf770 100644
--- a/pcbnew/drc/drc_rtree.h
+++ b/pcbnew/drc/drc_rtree.h
@@ -122,7 +122,18 @@ public:
         }
         else
         {
-            for( int layer : aItem->GetLayerSet().Seq() )
+            LSET layers = aItem->GetLayerSet();
+
+            // Special-case pad holes which pierce all the copper layers
+            if( aItem->Type() == PCB_PAD_T )
+            {
+                PAD* pad = static_cast<PAD*>( aItem );
+
+                if( pad->GetDrillSizeX() > 0 && pad->GetDrillSizeY() > 0 )
+                    layers |= LSET::AllCuMask();
+            }
+
+            for( int layer : layers.Seq() )
                 addLayer( (PCB_LAYER_ID) layer );
         }
     }
diff --git a/pcbnew/drc/drc_test_provider.cpp b/pcbnew/drc/drc_test_provider.cpp
index 4d80eb7896..634985f2bf 100644
--- a/pcbnew/drc/drc_test_provider.cpp
+++ b/pcbnew/drc/drc_test_provider.cpp
@@ -263,7 +263,9 @@ int DRC_TEST_PROVIDER::forEachGeometryItem( const std::vector<KICAD_T>& aTypes,
         {
             for( PAD* pad : footprint->Pads() )
             {
-                if( ( pad->GetLayerSet() & aLayers ).any() )
+                // Careful: if a pad has a hole then it pierces all layers
+                if( ( pad->GetDrillSizeX() > 0 && pad->GetDrillSizeY() > 0 )
+                        || ( pad->GetLayerSet() & aLayers ).any() )
                 {
                     if( !aFunc( pad ) )
                         return n;
diff --git a/pcbnew/tools/board_inspection_tool.cpp b/pcbnew/tools/board_inspection_tool.cpp
index a27c7e582a..5ac6c41e5e 100644
--- a/pcbnew/tools/board_inspection_tool.cpp
+++ b/pcbnew/tools/board_inspection_tool.cpp
@@ -282,6 +282,13 @@ int BOARD_INSPECTION_TOOL::InspectClearance( const TOOL_EVENT& aEvent )
     BOARD_ITEM* a = static_cast<BOARD_ITEM*>( selection.GetItem( 0 ) );
     BOARD_ITEM* b = static_cast<BOARD_ITEM*>( selection.GetItem( 1 ) );
 
+    auto hasHole =
+            []( BOARD_ITEM* aItem )
+            {
+                PAD* pad = dynamic_cast<PAD*>( aItem );
+                return pad && pad->GetDrillSizeX() > 0 && pad->GetDrillSizeY() > 0;
+            };
+
     wxCHECK( a && b, 0 );
 
     if( a->Type() == PCB_GROUP_T )
@@ -322,16 +329,16 @@ int BOARD_INSPECTION_TOOL::InspectClearance( const TOOL_EVENT& aEvent )
     {
         PAD* pad = static_cast<PAD*>( a );
 
-        if( pad->GetAttribute() == PAD_ATTRIB_SMD && pad->IsOnLayer( F_Cu ) )
+        if( pad->IsOnLayer( F_Cu ) )
             layer = F_Cu;
         else
             layer = B_Cu;
     }
-    else if( b->Type() == PCB_PAD_T )
+    else if( b->Type() == PCB_PAD_T && static_cast<PAD*>( a )->GetAttribute() == PAD_ATTRIB_SMD )
     {
         PAD* pad = static_cast<PAD*>( b );
 
-        if( pad->GetAttribute() == PAD_ATTRIB_SMD && pad->IsOnLayer( F_Cu ) )
+        if( pad->IsOnLayer( F_Cu ) )
             layer = F_Cu;
         else
             layer = B_Cu;
@@ -356,15 +363,45 @@ int BOARD_INSPECTION_TOOL::InspectClearance( const TOOL_EVENT& aEvent )
     }
     else if( !( a->GetLayerSet() & LSET( 3, layer, Edge_Cuts, Margin ) ).any() )
     {
-        r->Report( wxString::Format( _( "%s not present on layer %s.  No clearance defined." ),
-                                     a->GetSelectMenuText( r->GetUnits() ),
-                                     m_frame->GetBoard()->GetLayerName( layer ) ) );
+        if( hasHole( a ) )
+        {
+            r->Report( "<h7>" + _( "Hole clearance resolution for:" ) + "</h7>" );
+
+            r->Report( wxString::Format( "<ul><li>%s %s</li><li>%s</li><li>%s</li></ul>",
+                                         _( "Layer" ),
+                                         EscapeHTML( m_frame->GetBoard()->GetLayerName( layer ) ),
+                                         EscapeHTML( getItemDescription( a ) ),
+                                         EscapeHTML( getItemDescription( b ) ) ) );
+
+            reportClearance( HOLE_CLEARANCE_CONSTRAINT, layer, a, b, r );
+        }
+        else
+        {
+            r->Report( wxString::Format( _( "%s not present on layer %s.  No clearance defined." ),
+                                         a->GetSelectMenuText( r->GetUnits() ),
+                                         m_frame->GetBoard()->GetLayerName( layer ) ) );
+        }
     }
     else if( !( b->GetLayerSet() & LSET( 3, layer, Edge_Cuts, Margin ) ).any() )
     {
-        r->Report( wxString::Format( _( "%s not present on layer %s.  No clearance defined." ),
-                                     b->GetSelectMenuText( r->GetUnits() ),
-                                     m_frame->GetBoard()->GetLayerName( layer ) ) );
+        if( hasHole( b ) )
+        {
+            r->Report( "<h7>" + _( "Hole clearance resolution for:" ) + "</h7>" );
+
+            r->Report( wxString::Format( "<ul><li>%s %s</li><li>%s</li><li>%s</li></ul>",
+                                         _( "Layer" ),
+                                         EscapeHTML( m_frame->GetBoard()->GetLayerName( layer ) ),
+                                         EscapeHTML( getItemDescription( b ) ),
+                                         EscapeHTML( getItemDescription( a ) ) ) );
+
+            reportClearance( HOLE_CLEARANCE_CONSTRAINT, layer, b, a, r );
+        }
+        else
+        {
+            r->Report( wxString::Format( _( "%s not present on layer %s.  No clearance defined." ),
+                                         b->GetSelectMenuText( r->GetUnits() ),
+                                         m_frame->GetBoard()->GetLayerName( layer ) ) );
+        }
     }
     else if( a->GetLayer() == Edge_Cuts || a->GetLayer() == Margin
                 || b->GetLayer() == Edge_Cuts || b->GetLayer() == Margin )