Abstract: A method and system for optimizing branch prediction in an executable computer program compiled for execution on a pipelined processor that employs branch prediction. The source program is compiled and, in one embodiment, instrumented to collect branch selection statistics. The compiled program is run and statistics collected using the instrumentation or a standard trace program. The branch statistics are used to modify the executable program to cause branch prediction to be correct a majority of the time for the workload against which the program was run. In a computer system having a branch prediction bit, that bit is set or cleared to cause correct branch prediction a majority of the time.