diff --git a/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/preferences/impl/PreferencesManagerImpl.java b/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/preferences/impl/PreferencesManagerImpl.java
index 55c7e5a4a5..5b9237f6cb 100644
--- a/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/preferences/impl/PreferencesManagerImpl.java
+++ b/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/preferences/impl/PreferencesManagerImpl.java
@@ -42,6 +42,7 @@ import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -151,11 +152,7 @@ class PreferencesManagerImpl implements IPreferencesManager {
      * @see net.sourceforge.pmd.runtime.preferences.IPreferencesManager#setRuleSet(net.sourceforge.pmd.RuleSet)
      */
     public void setRuleSet(RuleSet newRuleSet) {
-        Set newRules = getNewRules(newRuleSet);
-        if (!newRules.isEmpty()) {
-            addNewRulesToConfiguredProjects(newRules);
-        }
-
+        updateConfiguredProjects(newRuleSet);
         ruleSet = newRuleSet;
         storeRuleSetInStateLocation(ruleSet);
     }
@@ -356,12 +353,13 @@ class PreferencesManagerImpl implements IPreferencesManager {
     }
 
     /**
-     * Add new rules to already configured projects
+     * Add new rules to already configured projects, and update the exclude/include patterns
      */
-    private void addNewRulesToConfiguredProjects(Set addedRules) {
-        log.debug("Add new rules to configured projects");
+    private void updateConfiguredProjects(RuleSet updatedRuleSet) {
+    	log.debug("Updating configured projects");
         RuleSet addedRuleSet = new RuleSet();
-        Iterator ruleIterator = addedRules.iterator();
+        Set newRules = getNewRules(updatedRuleSet);
+        Iterator ruleIterator = newRules.iterator();
         while (ruleIterator.hasNext()) {
             Rule rule = (Rule) ruleIterator.next();
             addedRuleSet.addRule(rule);
@@ -377,6 +375,9 @@ class PreferencesManagerImpl implements IPreferencesManager {
                     RuleSet projectRuleSet = properties.getProjectRuleSet();
                     if (projectRuleSet != null) {
                         projectRuleSet.addRuleSet(addedRuleSet);
+                        projectRuleSet.setExcludePatterns(new ArrayList(updatedRuleSet.getExcludePatterns()));
+                        projectRuleSet.setIncludePatterns(new ArrayList(updatedRuleSet.getIncludePatterns()));
+                        properties.setProjectRuleSet(projectRuleSet);
                         properties.sync();
                     }
                 } catch (PropertiesException e) {
diff --git a/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/ProjectPropertiesManagerImpl.java b/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/ProjectPropertiesManagerImpl.java
index 4f1e9c6377..612c7b3fa2 100644
--- a/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/ProjectPropertiesManagerImpl.java
+++ b/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/ProjectPropertiesManagerImpl.java
@@ -318,13 +318,16 @@ public class ProjectPropertiesManagerImpl implements IProjectPropertiesManager {
         bean.setIncludeDerivedFiles(projectProperties.isIncludeDerivedFiles());
 
         if (!projectProperties.isRuleSetStoredInProject()) {
+        	final RuleSet ruleSet = projectProperties.getProjectRuleSet();
             final List rules = new ArrayList();
-            final Iterator i = projectProperties.getProjectRuleSet().getRules().iterator();
+            final Iterator i = ruleSet.getRules().iterator();
             while (i.hasNext()) {
                 final Rule rule = (Rule) i.next();
                 rules.add(new RuleSpecTO(rule.getName(), rule.getRuleSetName())); // NOPMD:AvoidInstantiatingObjectInLoop
             }
             bean.setRules((RuleSpecTO[]) rules.toArray(new RuleSpecTO[rules.size()]));
+            bean.setExcludePatterns((String[])ruleSet.getExcludePatterns().toArray(new String[ruleSet.getExcludePatterns().size()]));
+            bean.setIncludePatterns((String[])ruleSet.getIncludePatterns().toArray(new String[ruleSet.getIncludePatterns().size()]));
         }
 
         return bean;
diff --git a/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/ProjectPropertiesTO.java b/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/ProjectPropertiesTO.java
index 5d51aeec68..a9b7232cd6 100644
--- a/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/ProjectPropertiesTO.java
+++ b/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/ProjectPropertiesTO.java
@@ -63,6 +63,8 @@ package net.sourceforge.pmd.runtime.properties.impl;
  */
 public class ProjectPropertiesTO {
     private RuleSpecTO[] rules;
+    private String[] excludePatterns;
+    private String[] includePatterns;
     private String workingSetName;
     private boolean ruleSetStoredInProject;
     private String ruleSetFile;
@@ -86,6 +88,40 @@ public class ProjectPropertiesTO {
     }
     
     /**
+     * @return an array of String objects for exclude patterns
+     * for the current project.
+     */
+    public String[] getExcludePatterns() {
+		return excludePatterns;
+	}
+    
+    /**
+     * Set the exclude patterns for a project
+     * @param excludePatterns an array of String objects for exclude patterns
+     * for the current project.
+     */
+	public void setExcludePatterns(String[] excludePatterns) {
+		this.excludePatterns = excludePatterns;
+	}
+
+    /**
+     * @return an array of String objects for include patterns
+     * for the current project.
+     */
+	public String[] getIncludePatterns() {
+		return includePatterns;
+	}
+
+    /**
+     * Set the include patterns for a project
+     * @param includePatterns an array of String objects for include patterns
+     * for the current project.
+     */
+	public void setIncludePatterns(String[] includePatterns) {
+		this.includePatterns = includePatterns;
+	}
+
+	/**
      * @return ruleSetStoredInProject tells whether the project use a ruleset
      * stored in the project or the global plugin ruleset.
      */
diff --git a/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/mapping.xml b/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/mapping.xml
index c1b9f47be6..f4b5240308 100644
--- a/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/mapping.xml
+++ b/pmd-eclipse-plugin/pmd-eclipse-runtime/src/net/sourceforge/pmd/runtime/properties/impl/mapping.xml
@@ -27,6 +27,22 @@
                         <bind-xml name="ruleSetFile" node="element"/>
                 </field>
 
+                <field name="ExcludePatterns"
+                       type="java.lang.String"
+                       collection="array"
+                       get-method="getExcludePatterns"
+                       set-method="setExcludePatterns">
+                        <bind-xml name="excludePattern" location="excludePatterns" node="element"/>
+                </field>
+
+                <field name="IncludePatterns"
+                       type="java.lang.String"
+                       collection="array"
+                       get-method="getIncludePatterns"
+                       set-method="setIncludePatterns">
+                        <bind-xml name="includePattern" location="includePatterns" node="element"/>
+                </field>
+
                 <field name="Rules"
                        type="net.sourceforge.pmd.runtime.properties.impl.RuleSpecTO"
                        collection="array"