diff --git a/Doxyfile b/doc/Doxyfile
similarity index 99%
rename from Doxyfile
rename to doc/Doxyfile
index 2d1dab711..16940c2bd 100644
--- a/Doxyfile
+++ b/doc/Doxyfile
@@ -52,7 +52,7 @@ PROJECT_LOGO           =
 # If a relative path is entered, it will be relative to the location 
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = doc
+OUTPUT_DIRECTORY       = .
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create 
 # 4096 sub-directories (in 2 levels) under the output directory of each output 
@@ -638,19 +638,19 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = gtsam/base \
-                         gtsam/geometry \
-                         gtsam/inference \
-                         gtsam/discrete \
-                         gtsam/linear \
-                         gtsam/nonlinear \
-                         gtsam
-#                         gtsam/slam \
-#                         gtsam_unstable/slam \
-#                         gtsam_unstable/base \
-#                         gtsam_unstable/geometry \
-#                         gtsam_unstable/dynamics \
-#                         gtsam_unstable 
+INPUT                  = ../gtsam/base \
+                         ../gtsam/geometry \
+                         ../gtsam/inference \
+                         ../gtsam/discrete \
+                         ../gtsam/linear \
+                         ../gtsam/nonlinear \
+                         ../gtsam
+#                         ../gtsam/slam \
+#                         ../gtsam_unstable/slam \
+#                         ../gtsam_unstable/base \
+#                         ../gtsam_unstable/geometry \
+#                         ../gtsam_unstable/dynamics \
+#                         ../gtsam_unstable 
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
diff --git a/DoxygenLayout.xml b/doc/DoxygenLayout.xml
similarity index 100%
rename from DoxygenLayout.xml
rename to doc/DoxygenLayout.xml
diff --git a/makedoc.sh b/makedoc.sh
index 5acbd3d87..8de348fa5 100755
--- a/makedoc.sh
+++ b/makedoc.sh
@@ -9,5 +9,5 @@ PATH=$PATH:/Applications/Doxygen.app/Contents/Resources
 # directory, so that the output 'doc' goes in the gtsam directory.
 
 GTSAM_DIR=$(dirname "$0")
-cd $GTSAM_DIR
+cd $GTSAM_DIR/doc
 doxygen
\ No newline at end of file