man I had some serious problems running java in cygwin with a shell script (sh script)… So I am going to post my script to help you out… there are a couple things of note first… java a windows program expects windows paths your cygwin script proably uses unix paths. cygwin sh scripts treat ‘;’ as a special character so when using multiple classpaths you must escape it ‘\;’ to make it work as expected… # test.shJAVAEXE=$JAVA_HOME/bin/java.execd ../IEP_HOME=C:\dev\dsmayer\sandbox\iepIEP_BIN=C:\dev\dsmayer\sandbox\iep\binIEP_LIB=C:\dev\dsmayer\sandbox\iep\libIEP_JAR=C:\dev\dsmayer\sandbox\iep\lib\iepio.jarIEP_IST=C:\dev\dsmayer\sandbox\iep\lib\istcustom.jarIEPB_JAR=C:\dev\dsmayer\sandbox\iep\lib\backport-util-concurrent.jarIEP_PROPS=C:\dev\dsmayer\sandbox\iep\properties echo java -cp $IEP_JAR\;$IEP_IST\;$IEPB_JAR RCS.example.RCSregechojava -cp $IEP_JAR\;$IEP_IST\;$IEPB_JAR RCS.example.RCSreg &java -cp $IEP_PROPS\;$IEP_JAR\;$IEPB_JAR\;$IEP_IST RCS.example.clients.ResourceClient &java -cp $IEP_PROPS\;$IEP_JAR\;$IEPB_JAR\;$IEP_IST RCS.example.clients.UserClient &