diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
index affddd6eaa34249f7edc302fc5431d3a569f7e23..f6b0188e76a0db963f316887da82ea2c6891edc2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
@@ -109,7 +109,7 @@ public class LayerXmlParser {
         result.append(layerToXml(layer, new HashSet<>()));
       }
     }
-    if (!compartmentsAdded) {
+    if (!compartmentsAdded && pathways.size() > 0) {
       Layer layer = new Layer();
       layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
       result.append(layerToXml(layer, pathways));