diff --git a/Makefile.am b/Makefile.am
index 8f21a031..29000f24 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -16,7 +16,7 @@ TESTS = unit_tests io_unit_tests
 check_PROGRAMS = unit_tests dEploid_dbg dEploid_prof io_unit_tests
 PROG = DEPLOID
 
-common_flags = -std=c++0x -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\"
+common_flags = -std=c++0x -Isrc/ -DDEPLOIDVERSION=\"${DEPLOIDVERSION}\" -DLASSOVERSION=\"${LASSOVERSION}\" -DCOMPILEDATE=\"${COMPILEDATE}\"
 common_LDADD = -lz
 
 common_src = src/random/fastfunc.cpp \
diff --git a/src/codeCogs/randomSample.hpp b/src/codeCogs/randomSample.hpp
index 5263e75a..1eb6473a 100644
--- a/src/codeCogs/randomSample.hpp
+++ b/src/codeCogs/randomSample.hpp
@@ -15,7 +15,7 @@
 #define STATS_DISTS_CONTINUOUS_NORMAL_RANDOMSAMPLE_H
 
 #include <math.h>
-#include "src/codeCogs/mersenne.hpp"
+#include "codeCogs/mersenne.hpp"
 
 #define NORMALDENS(x) ((fabs(x) > 8.0) ? 0 : 0.398942280 * exp(- x * x / 2))
 
diff --git a/src/debug/mcmcDebug.cpp b/src/debug/mcmcDebug.cpp
index 48fd9f0c..f0670e60 100644
--- a/src/debug/mcmcDebug.cpp
+++ b/src/debug/mcmcDebug.cpp
@@ -23,7 +23,7 @@
  *
  */
 
-#include "src/mcmc.hpp"
+#include "mcmc.hpp"
 
 
 bool McmcMachinery::doutProp() {
diff --git a/src/debug/vcfReaderDebug.cpp b/src/debug/vcfReaderDebug.cpp
index a6c5d090..7085f7b4 100644
--- a/src/debug/vcfReaderDebug.cpp
+++ b/src/debug/vcfReaderDebug.cpp
@@ -24,8 +24,8 @@
  */
 
 #include <iostream>      // std::cout
-#include "src/global.h"
-#include "src/vcfReader.hpp"
+#include "global.h"
+#include "vcfReader.hpp"
 
 using std::endl;
 
diff --git a/src/export/dEploidIOExport.cpp b/src/export/dEploidIOExport.cpp
index 1d9ec077..843ba8f9 100644
--- a/src/export/dEploidIOExport.cpp
+++ b/src/export/dEploidIOExport.cpp
@@ -23,8 +23,8 @@
  *
  */
 
-#include "src/dEploidIO.hpp"
-#include "src/mcmc.hpp"
+#include "dEploidIO.hpp"
+#include "mcmc.hpp"
 
 
 void DEploidIO::wrapUp(){
diff --git a/src/export/dEploidIOExportPosteriorProb.cpp b/src/export/dEploidIOExportPosteriorProb.cpp
index b8f68df3..39872c70 100644
--- a/src/export/dEploidIOExportPosteriorProb.cpp
+++ b/src/export/dEploidIOExportPosteriorProb.cpp
@@ -23,9 +23,9 @@
  *
  */
 
-#include "src/dEploidIO.hpp"
-#include "src/updateHap.hpp"
-#include "src/mcmc.hpp"
+#include "dEploidIO.hpp"
+#include "updateHap.hpp"
+#include "mcmc.hpp"
 
 void McmcMachinery::writeLastFwdProb(bool useIBD){
     if ( this->dEploidIO_ ->doExportPostProb() != true ){
diff --git a/src/export/writeMcmcRelated.cpp b/src/export/writeMcmcRelated.cpp
index eed1407a..5146fa9b 100644
--- a/src/export/writeMcmcRelated.cpp
+++ b/src/export/writeMcmcRelated.cpp
@@ -23,8 +23,8 @@
  *
  */
 
-#include "src/dEploidIO.hpp"
-#include "src/mcmc.hpp"
+#include "dEploidIO.hpp"
+#include "mcmc.hpp"
 
 void DEploidIO::writeMcmcRelated (McmcSample * mcmcSample, bool useIBD){
     this->writeProp( mcmcSample, useIBD );
diff --git a/src/gzstream/gzstream.cpp b/src/gzstream/gzstream.cpp
index c215885d..6bb16283 100644
--- a/src/gzstream/gzstream.cpp
+++ b/src/gzstream/gzstream.cpp
@@ -28,7 +28,7 @@
 
 #include <iostream>
 #include <string.h>  // for memcpy
-#include "src/gzstream/gzstream.h"
+#include "gzstream/gzstream.h"
 
 #ifdef GZSTREAM_NAMESPACE
 namespace GZSTREAM_NAMESPACE {
diff --git a/src/utility.cpp b/src/utility.cpp
index f25de9de..26148afd 100644
--- a/src/utility.cpp
+++ b/src/utility.cpp
@@ -23,12 +23,12 @@
  *
  */
 
-#include "src/utility.hpp"
+#include "utility.hpp"
 #include <iterator>     // std::distance
 #include <algorithm> // find
-#include "src/codeCogs/loggammasum.h" // which includes log_gamma.h
-#include "src/codeCogs/gamma.h"
-#include "src/codeCogs/logbeta.h"
+#include "codeCogs/loggammasum.h" // which includes log_gamma.h
+#include "codeCogs/gamma.h"
+#include "codeCogs/logbeta.h"
 
 
 
diff --git a/src/variantIndex.hpp b/src/variantIndex.hpp
index 790399da..a155a406 100644
--- a/src/variantIndex.hpp
+++ b/src/variantIndex.hpp
@@ -30,7 +30,7 @@
 #include <vector>
 #include <string>
 #include <cassert>
-#include "src/global.h"
+#include "global.h"
 
 
 using std::vector;