diff --git a/spec/pane-container-model-spec.coffee b/spec/pane-container-model-spec.coffee
index a37772d7d..027272218 100644
--- a/spec/pane-container-model-spec.coffee
+++ b/spec/pane-container-model-spec.coffee
@@ -6,10 +6,16 @@ describe "PaneContainerModel", ->
     [containerA, pane1A, pane2A, pane3A] = []
 
     beforeEach ->
-      pane1A = new PaneModel
+      # This is a dummy item to prevent panes from being empty on deserialization
+      class Item
+        atom.deserializers.add(this)
+        @deserialize: -> new this
+        serialize: -> deserializer: 'Item'
+
+      pane1A = new PaneModel(items: [new Item])
       containerA = new PaneContainerModel(root: pane1A)
-      pane2A = pane1A.splitRight()
-      pane3A = pane2A.splitDown()
+      pane2A = pane1A.splitRight(items: [new Item])
+      pane3A = pane2A.splitDown(items: [new Item])
 
     it "preserves the focused pane across serialization", ->
       expect(pane3A.focused).toBe true
diff --git a/spec/pane-container-spec.coffee b/spec/pane-container-spec.coffee
index 5fb759860..374b84a00 100644
--- a/spec/pane-container-spec.coffee
+++ b/spec/pane-container-spec.coffee
@@ -130,7 +130,7 @@ describe "PaneContainer", ->
       expect(newContainer.find('.pane-row > :contains(1)').width()).toBe 150
       expect(newContainer.find('.pane-row > .pane-column > :contains(2)').height()).toBe 100
 
-    xit "removes empty panes on deserialization", ->
+    it "removes empty panes on deserialization", ->
       # only deserialize pane 1's view successfully
       TestView.deserialize = ({name}) -> new TestView(name) if name is '1'
       newContainer = atom.deserializers.deserialize(container.serialize())
diff --git a/src/pane-container-model.coffee b/src/pane-container-model.coffee
index 81f93df64..f7fa4c0c6 100644
--- a/src/pane-container-model.coffee
+++ b/src/pane-container-model.coffee
@@ -16,12 +16,14 @@ class PaneContainerModel extends Model
   @behavior 'activePaneItem', ->
     @$activePane.switch (activePane) -> activePane?.$activeItem
 
-  constructor: ->
+  constructor: (params) ->
     super
     @subscribe @$root, @onRootChanged
+    @destroyEmptyPanes() if params?.destroyEmptyPanes
 
   deserializeParams: (params) ->
     params.root = atom.deserializers.deserialize(params.root, container: this)
+    params.destroyEmptyPanes = true
     params
 
   serializeParams: (params) ->
@@ -59,3 +61,6 @@ class PaneContainerModel extends Model
       @subscribe root, 'destroyed', =>
         @activePane = null
         @root = null
+
+  destroyEmptyPanes: ->
+    pane.destroy() for pane in @getPanes() when pane.items.length is 0
diff --git a/src/pane-container.coffee b/src/pane-container.coffee
index 6c03ddbe2..4b258ff7d 100644
--- a/src/pane-container.coffee
+++ b/src/pane-container.coffee
@@ -110,10 +110,6 @@ class PaneContainer extends View
       return pane if view?
     null
 
-  removeEmptyPanes: ->
-    for pane in @getPanes() when pane.getItems().length == 0
-      pane.remove()
-
   focusNextPane: ->
     panes = @getPanes()
     if panes.length > 1
diff --git a/src/pane-model.coffee b/src/pane-model.coffee
index 66b231f85..4866e068b 100644
--- a/src/pane-model.coffee
+++ b/src/pane-model.coffee
@@ -53,7 +53,7 @@ class PaneModel extends Model
   # Private: Called by the Serializable mixin during deserialization.
   deserializeParams: (params) ->
     {items, activeItemUri} = params
-    params.items = items.map (itemState) -> atom.deserializers.deserialize(itemState)
+    params.items = compact(items.map (itemState) -> atom.deserializers.deserialize(itemState))
     params.activeItem = find params.items, (item) -> item.getUri?() is activeItemUri
     params