diff --git a/compiler/compile.go b/compiler/compile.go
index 131cbd2..3bbaf12 100644
--- a/compiler/compile.go
+++ b/compiler/compile.go
@@ -46,14 +46,9 @@ func CompileDir(path string, opts *settings.Settings) {
 			)
 			switch filepath.Ext(scores[i].Path) {
 			case ".ly":
-				msg, err = Lilypond(scores[i].Path)
+				msg, err = Lilypond(&scores[i])
 			case ".pdf":
-				if helpers.Exists(scores[i].OutputPath) {
-					os.Remove(scores[i].OutputPath)
-				}
-				if err == nil {
-					err = os.Link(scores[i].Path, scores[i].OutputPath)
-				}
+				err = linkPDF(&scores[i])
 			}
 
 			if err != nil {
@@ -108,3 +103,15 @@ func generateScores() func(string, os.FileInfo) error {
 		return nil
 	}
 }
+
+func linkPDF(s *settings.Score) (err error) {
+	err = helpers.ExistsOrCreate(filepath.Dir(s.OutputPath))
+	if err != nil {
+		return err
+	}
+	if helpers.Exists(s.OutputPath) {
+		os.Remove(s.OutputPath)
+	}
+	err = os.Link(s.Path, s.OutputPath)
+	return
+}
diff --git a/compiler/lilypond.go b/compiler/lilypond.go
index 6caf1c5..e505777 100644
--- a/compiler/lilypond.go
+++ b/compiler/lilypond.go
@@ -15,8 +15,8 @@
 package compiler
 
 import (
-	"os"
 	"os/exec"
+	"path/filepath"
 
 	log "github.com/Sirupsen/logrus"
 	"github.com/jjdekker/ponder/helpers"
@@ -37,21 +37,21 @@ func PrepareLilypond(opts *settings.Settings) {
 	}
 	lilypondArgs = append(lilypondArgs, "--loglevel=ERROR")
 	lilypondArgs = append(lilypondArgs, "--pdf")
-
-	lilypondArgs = append(lilypondArgs, "--output="+opts.OutputDir)
-	if !helpers.Exists(opts.OutputDir) {
-		log.WithFields(log.Fields{"path": opts.OutputDir}).Info("creating output directory")
-		err := os.MkdirAll(opts.OutputDir, os.ModePerm)
-		helpers.Check(err, "Could not create output directory")
-	}
 }
 
 // Lilypond runs the lilypond compiler on the given path
 // using the arguments prepared by the PrepareLilypond function
-func Lilypond(path string) (string, error) {
-	cmd := exec.Command(lilypondCmd, append(lilypondArgs, path)...)
+func Lilypond(s *settings.Score) (string, error) {
+	args := append(lilypondArgs, "--output="+filepath.Dir(s.OutputPath))
+	err := helpers.ExistsOrCreate(filepath.Dir(s.OutputPath))
+	if err != nil {
+		return "", err
+	}
+	args = append(args, s.Path)
+
+	cmd := exec.Command(lilypondCmd, args...)
 	log.WithFields(log.Fields{
-		"path": path,
+		"path": s.Path,
 		"cmd":  cmd,
 	}).Info("compiling file using lilypond")
 	out, err := cmd.CombinedOutput()
diff --git a/helpers/file_utils.go b/helpers/file_utils.go
index a584e33..b830c57 100644
--- a/helpers/file_utils.go
+++ b/helpers/file_utils.go
@@ -55,6 +55,15 @@ func Exists(path string) bool {
 	return false
 }
 
+// ExistsOrCreate will create a directory unless it already Exists
+func ExistsOrCreate(path string) (err error) {
+	if !Exists(path) {
+		log.WithFields(log.Fields{"path": path}).Info("creating directory")
+		err = os.MkdirAll(path, os.ModePerm)
+	}
+	return
+}
+
 // LastModified returns the time the file on the path was last modified,
 // if file lookup fails the current time is returned.
 func LastModified(path string) time.Time {
diff --git a/settings/score.go b/settings/score.go
index 3b50d5c..cc9b5c8 100644
--- a/settings/score.go
+++ b/settings/score.go
@@ -141,7 +141,11 @@ func (s *Score) GenerateOutputPath(opts *Settings) {
 		return
 	}
 	file = file[:dot+1] + "pdf"
-	s.OutputPath = filepath.Join(opts.OutputDir, file)
+	s.OutputPath = opts.OutputDir
+	if !opts.FlatOutputDir && len(s.Categories) > 0 {
+		s.OutputPath = filepath.Join(s.OutputPath, s.Categories[0])
+	}
+	s.OutputPath = filepath.Join(s.OutputPath, file)
 }
 
 // Scores aliases a slice of scores
diff --git a/settings/settings.go b/settings/settings.go
index a7d7a5f..cc7a4d1 100644
--- a/settings/settings.go
+++ b/settings/settings.go
@@ -38,6 +38,7 @@ type Settings struct {
 	BookScoreTempl       string   // Override for the partial book template placing scores
 	LatexResources       []string // Files to be copied to compile the book template
 	KeepBookTemplate     bool     // Leave the LaTeX source for the book in the output directory
+	FlatOutputDir        bool     // Keep all output file in a flat output directory
 }
 
 // FromFile reads a settings file in json format and returns the Settings struct