diff --git a/modules/Bio/EnsEMBL/VEP/Config.pm b/modules/Bio/EnsEMBL/VEP/Config.pm
index 76c359b9c..d29eab325 100755
--- a/modules/Bio/EnsEMBL/VEP/Config.pm
+++ b/modules/Bio/EnsEMBL/VEP/Config.pm
@@ -696,7 +696,14 @@ sub new {
     next if !defined($value) || (ref($value) eq "ARRAY" && @{$value} == 0) || grep { /$flag/ } @skip_opts;
 
     $value = join(" --$flag ", @{$value}) if ref($value) eq "ARRAY";
-    $value =~ s/(\/[\w-]+?)+\//\[PATH\]\//g;
+    
+    if ($^O eq "MSWin32"){
+      $value =~ s/.+(?=\\)/\[PATH\]/g;
+    }
+    else {
+      $value =~ s/.+(?=\/)/\[PATH\]/g;
+    }
+    
     $config_command .= $value eq 1? "--$flag "  : "--$flag $value ";
   }
 
diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
index a3e73e86c..0a94afe34 100755
--- a/modules/Bio/EnsEMBL/VEP/Constants.pm
+++ b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -53,7 +53,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 109;
-our $VEP_SUB_VERSION = 2;
+our $VEP_SUB_VERSION = 3;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS