diff --git a/app/models/milestone.rb b/app/models/milestone.rb
index 6a2ca767030..39ab0b536a3 100644
--- a/app/models/milestone.rb
+++ b/app/models/milestone.rb
@@ -25,6 +25,7 @@ class Milestone < ActiveRecord::Base
 
   scope :active, -> { with_state(:active) }
   scope :closed, -> { with_state(:closed) }
+  scope :of_projects, ->(ids) { where(project_id: ids) }
 
   validates :title, presence: true
   validates :project, presence: true
diff --git a/db/migrate/20140416074002_add_index_on_iid.rb b/db/migrate/20140416074002_add_index_on_iid.rb
index cbd09082781..85269e2a03b 100644
--- a/db/migrate/20140416074002_add_index_on_iid.rb
+++ b/db/migrate/20140416074002_add_index_on_iid.rb
@@ -1,7 +1,32 @@
 class AddIndexOnIid < ActiveRecord::Migration
   def change
+    RemoveDuplicateIid.clean(Issue)
+    RemoveDuplicateIid.clean(MergeRequest, 'target_project_id')
+    RemoveDuplicateIid.clean(Milestone)
+
     add_index :issues, [:project_id, :iid], unique: true
     add_index :merge_requests, [:target_project_id, :iid], unique: true
     add_index :milestones, [:project_id, :iid], unique: true
   end
 end
+
+class RemoveDuplicateIid
+  def self.clean(klass, project_field = 'project_id')
+    duplicates = klass.find_by_sql("SELECT iid, #{project_field} FROM #{klass.table_name} GROUP BY #{project_field}, iid HAVING COUNT(*) > 1")
+
+    duplicates.each do |duplicate|
+      project_id = duplicate.send(project_field)
+      iid = duplicate.iid
+      items = klass.of_projects(project_id).where(iid: iid)
+
+      if items.size > 1
+        puts "Remove #{klass.name} duplicates for iid: #{iid} and project_id: #{project_id}"
+        items.shift
+        items.each do |item|
+          item.destroy
+          puts '.'
+        end
+      end
+    end
+  end
+end