diff --git a/hakyll.cabal b/hakyll.cabal
--- a/hakyll.cabal
+++ b/hakyll.cabal
@@ -1,5 +1,5 @@
 Name:               hakyll
-Version:            3.1.2.0
+Version:            3.1.2.1
 
 Synopsis:           A simple static site generator library.
 Description:        A simple static site generator library, mainly aimed at
diff --git a/src/Hakyll/Core/Run.hs b/src/Hakyll/Core/Run.hs
--- a/src/Hakyll/Core/Run.hs
+++ b/src/Hakyll/Core/Run.hs
@@ -46,8 +46,9 @@
     provider <- timed logger "Creating provider" $
         fileResourceProvider configuration
 
-    -- Fetch the old graph from the store
-    oldGraph <- fromMaybe mempty <$>
+    -- Fetch the old graph from the store. If we don't find it, we consider this
+    -- to be the first run
+    (firstRun, oldGraph) <- fromMaybe (True, mempty) . fmap ((,) False) <$>
         storeGet store "Hakyll.Core.Run.run" "dependencies"
 
     let ruleSet = runRules rules provider
@@ -61,6 +62,7 @@
                     , hakyllRoutes           = rulesRoutes ruleSet
                     , hakyllResourceProvider = provider
                     , hakyllStore            = store
+                    , hakyllFirstRun         = firstRun
                     }
 
     -- Run the program and fetch the resulting state
@@ -83,6 +85,7 @@
     , hakyllRoutes           :: Routes
     , hakyllResourceProvider :: ResourceProvider
     , hakyllStore            :: Store
+    , hakyllFirstRun         :: Bool
     }
 
 data RuntimeState = RuntimeState
@@ -105,6 +108,7 @@
     section logger "Adding new compilers"
     provider <- hakyllResourceProvider <$> ask
     store <- hakyllStore <$> ask
+    firstRun <- hakyllFirstRun <$> ask
 
     -- Old state information
     oldCompilers <- hakyllCompilers <$> get
@@ -124,9 +128,10 @@
     -- Check which items have been modified
     modified <- fmap S.fromList $ flip filterM (map fst newCompilers) $
         liftIO . resourceModified provider store . fromIdentifier
+    let checkModified = if firstRun then const True else (`S.member` modified)
 
     -- Create a new analyzer and append it to the currect one
-    let newAnalyzer = makeDependencyAnalyzer newGraph (`S.member` modified) $
+    let newAnalyzer = makeDependencyAnalyzer newGraph checkModified $
             analyzerPreviousGraph oldAnalyzer
         analyzer = mappend oldAnalyzer newAnalyzer