diff --git a/src/main/java/org/reactome/release/qa/check/StableIdentifierCheck.java b/src/main/java/org/reactome/release/qa/check/StableIdentifierCheck.java
index f42583b..30615fb 100644
--- a/src/main/java/org/reactome/release/qa/check/StableIdentifierCheck.java
+++ b/src/main/java/org/reactome/release/qa/check/StableIdentifierCheck.java
@@ -1,10 +1,6 @@
 package org.reactome.release.qa.check;
 
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 
 import org.gk.model.GKInstance;
 import org.gk.model.ReactomeJavaConstants;
@@ -23,64 +19,74 @@
 public class StableIdentifierCheck extends AbstractQACheck {
 
 	public StableIdentifierCheck() {
-    }
+	}
 	
 	@Override
 	public QAReport executeQACheck() throws Exception {
-	    QAReport report = new QAReport();
-	    report.setColumnHeaders("DBID", "DisplayName", "Issue", "LastAuthor");
-	    
-	    Collection<GKInstance> stableIds = dba.fetchInstancesByClass(ReactomeJavaConstants.StableIdentifier);
-	    dba.loadInstanceAttributeValues(stableIds, new String[] {ReactomeJavaConstants.identifier});
-	    Map<String, Set<GKInstance>> idToInsts = new HashMap<>();
-	    for (GKInstance stableId : stableIds) {
-	        if (isEscaped(stableId)) {
-	            continue;
-	        }
-	        String id = (String) stableId.getAttributeValue(ReactomeJavaConstants.identifier);
-	        if (id == null) {
-	            report.addLine(stableId.getDBID().toString(),
-	                           stableId.getDisplayName(),
-	                           "Missing identifier",
-	                           QACheckerHelper.getLastModificationAuthor(stableId));
-	            continue;
-	        }
-	        idToInsts.compute(id, (key, set) -> {
-	            if (set == null)
-	                set = new HashSet<>();
-	            set.add(stableId);
-	            return set;
-	        });
-	        // Check if this stableId is used
-	        Collection<GKInstance> referrers = stableId.getReferers(ReactomeJavaConstants.stableIdentifier);
-	        if (referrers == null || referrers.size() == 0) {
-	            report.addLine(stableId.getDBID().toString(), 
-	                    stableId.getDisplayName(), 
-	                    "Not used", 
-	                    QACheckerHelper.getLastModificationAuthor(stableId));
-	        }
-	        else if (referrers.size() > 1) {
-	            report.addLine(stableId.getDBID().toString(), 
-                        stableId.getDisplayName(), 
-                        "Referred more than once", 
-                        QACheckerHelper.getLastModificationAuthor(stableId));
-	        }
-	    }
-	    
-	    for (Collection<GKInstance> instances: idToInsts.values()) {
-	        if (instances.size() != 1) {
-	            for (GKInstance stableId: instances) {
-	                if (!isEscaped(stableId)) {
-	                    report.addLine(stableId.getDBID().toString(), 
-	                            stableId.getDisplayName(), 
-	                            "Duplicated identifier", 
-	                            QACheckerHelper.getLastModificationAuthor(stableId));
-	                } 
-	            }
-	        }
-	    }
-	    
-	    return report;
+		QAReport report = new QAReport();
+		report.setColumnHeaders("DBID", "DisplayName", "Issue", "LastAuthor");
+
+		Collection<GKInstance> stableIds = dba.fetchInstancesByClass(ReactomeJavaConstants.StableIdentifier);
+		dba.loadInstanceAttributeValues(stableIds, new String[] {ReactomeJavaConstants.identifier});
+		Map<String, Set<GKInstance>> idToInsts = new HashMap<>();
+		for (GKInstance stableId : stableIds) {
+			if (isEscaped(stableId)) {
+				continue;
+			}
+			String id = (String) stableId.getAttributeValue(ReactomeJavaConstants.identifier);
+			if (id == null) {
+				report.addLine(stableId.getDBID().toString(),
+							   stableId.getDisplayName(),
+							   "Missing identifier",
+							   QACheckerHelper.getLastModificationAuthor(stableId));
+				continue;
+			}
+			idToInsts.compute(id, (key, set) -> {
+				if (set == null)
+					set = new HashSet<>();
+				set.add(stableId);
+				return set;
+			});
+			// Check if this stableId is used by an existing instance or a deleted instance
+			Collection<GKInstance> instanceReferrers = stableId.getReferers(ReactomeJavaConstants.stableIdentifier);
+			Collection<GKInstance> deletedInstanceReferrers =
+				stableId.getReferers("deletedStableIdentifier");
+			Collection<GKInstance> referrers = new ArrayList<>();
+			if (instanceReferrers != null) {
+				referrers.addAll(instanceReferrers);
+			}
+			if (deletedInstanceReferrers != null) {
+				referrers.addAll(deletedInstanceReferrers);
+			}
+
+			if (referrers.size() == 0) {
+				report.addLine(stableId.getDBID().toString(),
+						stableId.getDisplayName(),
+						"Not used",
+						QACheckerHelper.getLastModificationAuthor(stableId));
+			}
+			else if (referrers.size() > 1) {
+				report.addLine(stableId.getDBID().toString(),
+						stableId.getDisplayName(),
+						"Referred more than once",
+						QACheckerHelper.getLastModificationAuthor(stableId));
+			}
+		}
+
+		for (Collection<GKInstance> instances: idToInsts.values()) {
+			if (instances.size() != 1) {
+				for (GKInstance stableId: instances) {
+					if (!isEscaped(stableId)) {
+						report.addLine(stableId.getDBID().toString(),
+								stableId.getDisplayName(),
+								"Duplicated identifier",
+								QACheckerHelper.getLastModificationAuthor(stableId));
+					}
+				}
+			}
+		}
+
+		return report;
 	}
 
 }