diff --git a/tools.descartes.pmx.console/src/tools/descartes/pmx/console/PMXCommandLine.java b/tools.descartes.pmx.console/src/tools/descartes/pmx/console/PMXCommandLine.java
index 600a42ac464a7759a18bf6c8326ca7a15e142ff5..043ebe39cf9e0a3aa649ac433ea83762b9e0c4b6 100644
--- a/tools.descartes.pmx.console/src/tools/descartes/pmx/console/PMXCommandLine.java
+++ b/tools.descartes.pmx.console/src/tools/descartes/pmx/console/PMXCommandLine.java
@@ -163,14 +163,14 @@ public class PMXCommandLine {
 
 	private PMXController createPMX() {
 		try {
-			String inputDir = getInputDir();
+			String[] inputDirs = getInputDirs();
 			Configuration pmxConfiguration = new Configuration();
 			AnalysisController analysisController = new AnalysisController(pmxConfiguration);
-			registerFSReader(analysisController, inputDir);
+			registerFSReader(analysisController, inputDirs);
 
 			String outputDir = commandLine.getOptionValue(CMD_LONG_OPT_OUTPUT_DIR);
 			if(outputDir == null){
-				outputDir = inputDir;
+				outputDir = inputDirs[0];
 				log.info("No output directory specified. Logging to input directory.");
 			}
 
@@ -194,25 +194,26 @@ public class PMXCommandLine {
 
 	}
 
-
-	private String getInputDir() {
-		String inputDir = commandLine.getOptionValue(CMD_LONG_OPT_INPUT_DIR);
-		if (inputDir == null) {
-			log.info("missing value for command line option '" + CMD_LONG_OPT_INPUT_DIR + "'");
-			System.exit(1);
-		} else if (!new File(inputDir).exists()) {
-			log.info("File does not exist: " + CMD_LONG_OPT_INPUT_DIR);
-			log.info("\tcurrent:" + System.getProperty("user.dir"));
-			log.info("\trequested:" +inputDir);
-			System.exit(1); // or other exit code?
+	private String[] getInputDirs() {
+		String inputDirCmd = commandLine.getOptionValue(CMD_LONG_OPT_INPUT_DIR);
+		String[] inputDirs = inputDirCmd.split(";");
+		for (int idx = 0; idx < inputDirs.length; idx++) {
+			final String inputDir = inputDirs[idx];
+			if (inputDir == null) {
+				log.info("missing value for command line option '" + CMD_LONG_OPT_INPUT_DIR + "'");
+				System.exit(1);
+			} else if (!new File(inputDir).exists()) {
+				log.info("File does not exist: " + CMD_LONG_OPT_INPUT_DIR);
+				log.info("\tcurrent:" + System.getProperty("user.dir"));
+				log.info("\trequested:" + inputDir);
+				System.exit(1); // or other exit code?
+			}
 		}
-		return inputDir;
+		return inputDirs;
 	}
 
-	private static FSReader registerFSReader(IAnalysisController analysisInstance, final String kiekerTraceFile) {
-		String[] inputDirs;
-		inputDirs = new String[1];
-		inputDirs[0] = kiekerTraceFile;
+	private static FSReader registerFSReader(IAnalysisController analysisInstance, final String[] kiekerTraceFile) {
+		final String[] inputDirs = kiekerTraceFile;
 
 //		if (new File(kiekerTraceFile).getName().startsWith("kieker-")) {
 //			inputDirs = new String[1];
@@ -322,7 +323,7 @@ public class PMXCommandLine {
 	private String parseOutputDir() {
 		String outputDir = commandLine.getOptionValue(CMD_LONG_OPT_OUTPUT_DIR);
 		if (outputDir == null) {
-			outputDir = getInputDir();
+			outputDir = getInputDirs()[0];
 			log.info("No output directory specified. Logging to input directory.");
 		}
 		return outputDir;