diff --git a/CHANGES.txt b/CHANGES.txt
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -1,6 +1,8 @@
 Changelog for Weeder
 
-0.1.10
+0.1.11, released 2017-12-29
+    #29, deal with case-insensitive FilePath on Windows
+0.1.10, released 2017-12-28
     Make --verbose print out the directory when running commands
     Don't report semigroups as unused on any platforms
 0.1.9, released 2017-12-07
diff --git a/src/Cabal.hs b/src/Cabal.hs
--- a/src/Cabal.hs
+++ b/src/Cabal.hs
@@ -29,7 +29,7 @@
         _ -> fail $ "Didn't find exactly 1 cabal file in " ++ dir
 
 -- | Return the (exposed Hi files, internal Hi files, not found)
-selectHiFiles :: FilePath -> Map.HashMap FilePath a -> CabalSection -> ([a], [a], [ModuleName])
+selectHiFiles :: FilePath -> Map.HashMap FilePathEq a -> CabalSection -> ([a], [a], [ModuleName])
 selectHiFiles distDir his sect@CabalSection{..} = (external, internal, bad1++bad2)
     where
         (bad1, external) = partitionEithers $
@@ -38,11 +38,11 @@
         (bad2, internal) = partitionEithers
             [findHi his sect $ Right x | x <- filter (not . isPathsModule) cabalOtherModules]
 
-        findHi :: Map.HashMap FilePath a -> CabalSection -> Either FilePath ModuleName -> Either ModuleName a
+        findHi :: Map.HashMap FilePathEq a -> CabalSection -> Either FilePath ModuleName -> Either ModuleName a
         findHi his cabal@CabalSection{..} name = maybe (Left mname) Right $ firstJust (`Map.lookup` his) poss
             where
                 mname = either takeFileName id name
-                poss = [ normalise $ joinPath (root : x : either (return . dropExtension) (splitOn ".") name) <.> "dump-hi"
+                poss = [ filePathEq $ joinPath (root : x : either (return . dropExtension) (splitOn ".") name) <.> "dump-hi"
                     | extra <- [".",distDir]
                     , root <- ["build" </> extra </> x </> (x ++ "-tmp") | Just x <- [cabalSectionTypeName cabalSectionType]] ++
                               ["build", "build" </> distDir </> "build"]
diff --git a/src/Hi.hs b/src/Hi.hs
--- a/src/Hi.hs
+++ b/src/Hi.hs
@@ -74,9 +74,9 @@
     mappend = (<>)
 
 -- | Don't expose that we're just using the filename internally
-newtype HiKey = HiKey FilePath deriving (Eq,Ord,Hashable)
+newtype HiKey = HiKey FilePathEq deriving (Eq,Ord,Hashable)
 
-hiParseDirectory :: FilePath -> IO (Map.HashMap FilePath HiKey, Map.HashMap HiKey Hi)
+hiParseDirectory :: FilePath -> IO (Map.HashMap FilePathEq HiKey, Map.HashMap HiKey Hi)
 hiParseDirectory dir = do
     whenLoud $ putStrLn $ "Reading hi directory " ++ dir
     files <- filter ((==) ".dump-hi" . takeExtension) <$> listFilesRecursive dir
@@ -92,7 +92,7 @@
             evaluate $ rnf res
             return (len, res)
         whenLoud $ putStrLn $ S.showLength len ++ " bytes in " ++ showDuration time
-        return (name, res)
+        return (filePathEq name, res)
     -- here we try and dedupe any identical Hi modules
     let keys = Map.fromList $ map (second HiKey . swap) his
     mp1 <- evaluate $ Map.fromList $ map (second (keys Map.!)) his
diff --git a/src/Util.hs b/src/Util.hs
--- a/src/Util.hs
+++ b/src/Util.hs
@@ -1,7 +1,8 @@
-{-# LANGUAGE GADTs, OverloadedStrings #-}
+{-# LANGUAGE GeneralizedNewtypeDeriving, OverloadedStrings #-}
 
 module Util(
     Str,
+    FilePathEq, filePathEq,
     PackageName, ModuleName, IdentName,
     parseHanging,
     parseHanging2, unindent2,
@@ -19,7 +20,9 @@
 import Data.List.Extra
 import Data.Tuple.Extra
 import System.Process
+import System.FilePath
 import System.Directory
+import System.Info.Extra
 import System.Console.CmdArgs.Verbosity
 import Str(Str)
 import qualified Str as S
@@ -68,6 +71,13 @@
 isHaskellCtor [] = False
 isHaskellCtor (x:xs) = isUpper x || x == ':'
 
+-- | Normal 'FilePath' has 'Eq' but it allows non-normalised paths
+--   and on Windows is case-sensitive even when the underlying file system isn't.
+newtype FilePathEq = FilePathEq FilePath
+    deriving (Hashable,Eq,Ord,Show)
+
+filePathEq :: FilePath -> FilePathEq
+filePathEq = FilePathEq . (if isWindows then lower else id) . normalise
 
 -- | Given a list of mappings, and an initial set, find which items can be reached
 reachable :: (Eq k, Hashable k) => (k -> [k]) -> [k] -> Set.HashSet k
diff --git a/weeder.cabal b/weeder.cabal
--- a/weeder.cabal
+++ b/weeder.cabal
@@ -1,7 +1,7 @@
 cabal-version:      >= 1.18
 build-type:         Simple
 name:               weeder
-version:            0.1.10
+version:            0.1.11
 license:            BSD3
 license-file:       LICENSE
 category:           Development