diff --git a/fasta.cabal b/fasta.cabal
--- a/fasta.cabal
+++ b/fasta.cabal
@@ -10,7 +10,7 @@
 -- PVP summary:      +-+------- breaking API changes
 --                   | | +----- non-breaking API additions
 --                   | | | +--- code changes with no API change
-version:             0.10.4.1
+version:             0.10.4.2
 
 -- A short (one-line) description of the package.
 synopsis:            A simple, mindless parser for fasta files.
diff --git a/src/Data/Fasta/ByteString/Lazy/Parse.hs b/src/Data/Fasta/ByteString/Lazy/Parse.hs
--- a/src/Data/Fasta/ByteString/Lazy/Parse.hs
+++ b/src/Data/Fasta/ByteString/Lazy/Parse.hs
@@ -171,12 +171,13 @@
   where
     toFasta x = FastaSequence { fastaHeader = B.fromChunks
                                             . take 1
-                                            . SB.lines
+                                            . lines'
                                             $ x
                               , fastaSeq    = B.fromChunks
                                             . tail
-                                            . SB.lines
+                                            . lines'
                                             $ x }
+    lines'    = SB.lines . SB.filter (/= '\r')
 
 -- | Parse a CLIP fasta file into strict text sequences for pipes.
 pipesCLIPFasta :: (MonadIO m)
diff --git a/src/Data/Fasta/ByteString/Parse.hs b/src/Data/Fasta/ByteString/Parse.hs
--- a/src/Data/Fasta/ByteString/Parse.hs
+++ b/src/Data/Fasta/ByteString/Parse.hs
@@ -168,8 +168,9 @@
                $ p )
            >-> P.map toFasta
   where
-    toFasta x = FastaSequence { fastaHeader = head . B.lines $ x
-                              , fastaSeq    = B.concat . tail . B.lines $ x }
+    toFasta x = FastaSequence { fastaHeader = head . lines' $ x
+                              , fastaSeq    = B.concat . tail . lines' $ x }
+    lines'    = B.lines . B.filter (/= '\r')
 
 -- | Parse a CLIP fasta file into strict text sequences for pipes.
 pipesCLIPFasta :: (MonadIO m)
diff --git a/src/Data/Fasta/Text/Lazy/Parse.hs b/src/Data/Fasta/Text/Lazy/Parse.hs
--- a/src/Data/Fasta/Text/Lazy/Parse.hs
+++ b/src/Data/Fasta/Text/Lazy/Parse.hs
@@ -167,12 +167,13 @@
   where
     toFasta x = FastaSequence { fastaHeader = T.fromChunks
                                             . take 1
-                                            . ST.lines
+                                            . lines'
                                             $ x
                               , fastaSeq    = T.fromChunks
                                             . tail
-                                            . ST.lines
+                                            . lines'
                                             $ x }
+    lines'    = ST.lines . ST.filter (/= '\r')
 
 -- | Parse a CLIP fasta file into a pipe
 pipesCLIPFasta :: (MonadIO m)
diff --git a/src/Data/Fasta/Text/Parse.hs b/src/Data/Fasta/Text/Parse.hs
--- a/src/Data/Fasta/Text/Parse.hs
+++ b/src/Data/Fasta/Text/Parse.hs
@@ -161,8 +161,9 @@
                                              $ p )
            >-> P.map toFasta
   where
-    toFasta x = FastaSequence { fastaHeader = head . T.lines $ x
-                              , fastaSeq    = T.concat . tail . T.lines $ x }
+    toFasta x = FastaSequence { fastaHeader = head . lines' $ x
+                              , fastaSeq    = T.concat . tail . lines' $ x }
+    lines'    = T.lines . T.filter (/= '\r')
 
 -- | Parse a CLIP fasta file into a pipe
 pipesCLIPFasta :: (MonadIO m)