A system and method for reorganizing source code using frequency based instruction loop replication are provided. Code is reorganized based on the frequency of execution of blocks of the code so as to favor frequently executed blocks of code over rarely executed code with regard to subsequent optimizations. Frequently executed blocks of instructions are maintained within loop/switch statements and rarely executed blocks of instructions are removed from the loop/switch statements. The rarely executed blocks of instructions may be replicated after the loop/switch statement with a reference back to the loop/switch statement. In this way, when subsequent loop/switch statement optimizations are applied, the frequently executed blocks of instructions within the loop are more likely to benefit from such optimizations since the negative influence of the rarely executed blocks of instructions has been removed.