diff --git a/instrument.c b/instrument.c
index d19b690..81b0bf9 100644
--- a/instrument.c
+++ b/instrument.c
@@ -70,7 +70,7 @@ static void check_contains_file(const char * file1, const char * file2) {
   }
 }
 
-static void instrument_file(const char * source_file, const char * destination_file, const char * id, int instrumenting) {
+static void instrument_file(const char * source_file, const char * destination_file, const char * id, int instrumenting, char * filepath) {
   if (g_verbose) {
     printf("Instrumenting file %s\n", id);
   }
@@ -108,7 +108,7 @@ static void instrument_file(const char * source_file, const char * destination_f
         else if (result == JSCOVERAGE_ERROR_INVALID_BYTE_SEQUENCE) {
           fatal("error decoding %s in file %s", jscoverage_encoding, id);
         }
-        jscoverage_instrument_js(id, characters, num_characters, output_stream);
+        jscoverage_instrument_js(filepath, characters, num_characters, output_stream);
         free(characters);
 
         if (fwrite(output_stream->data, 1, output_stream->length, output) != output_stream->length) {
@@ -135,7 +135,8 @@ void jscoverage_instrument(const char * source,
                            char ** exclude,
                            int num_exclude,
                            char ** no_instrument,
-                           int num_no_instrument)
+                           int num_no_instrument,
+                           char * path)
 {
   assert(source != NULL);
   assert(destination != NULL);
@@ -215,9 +216,20 @@ void jscoverage_instrument(const char * source,
       free(ni);
     }
 
-    instrument_file(s, d, p->name, instrument_this);
+    /** make sure the path does not end in a slash. **/
+    size_t length;
+    while (string_ends_with(path, "/")) {
+        length = strlen(path);
+        path[length-1] = '\0';
+    }
+
+    length = strlen(path) + strlen(p->name) + 2;
+    char * filepath = malloc(length);
+    snprintf(filepath, length, "%s/%s", path, p->name);
+    instrument_file(s, d, p->name, instrument_this, filepath);
 
   cleanup:
+    free(filepath);
     free(s);
     free(d);
   }
diff --git a/instrument.h b/instrument.h
index a8720b0..0df539f 100644
--- a/instrument.h
+++ b/instrument.h
@@ -26,6 +26,7 @@ void jscoverage_instrument(const char * source,
                            char ** exclude,
                            int num_exclude,
                            char ** no_instrument,
-                           int num_no_instrument);
+                           int num_no_instrument,
+                           char * path);
 
 #endif /* INSTRUMENT_H_ */
diff --git a/jscoverage.c b/jscoverage.c
index f011148..5fddd4a 100644
--- a/jscoverage.c
+++ b/jscoverage.c
@@ -126,17 +126,20 @@ int main(int argc, char ** argv) {
     fatal_command_line("missing argument");
   }
 
+  char * path;
+  path = strdup(source);
   source = make_canonical_path(source);
   destination = make_canonical_path(destination);
 
   jscoverage_init();
-  jscoverage_instrument(source, destination, verbose, exclude, num_exclude, no_instrument, num_no_instrument);
+  jscoverage_instrument(source, destination, verbose, exclude, num_exclude, no_instrument, num_no_instrument, path);
   jscoverage_cleanup();
 
   free(source);
   free(destination);
   free(exclude);
   free(no_instrument);
+  free(path);
 
   exit(EXIT_SUCCESS);
 }