The present invention provides for a method for computer program functional partitioning for heterogeneous multi-processing systems. At least one system parameter of a computer system comprising one or more disparate processing nodes is identified. Computer program code comprising a program to be run on the computer system is received. A whole program representation is generated based on received computer program code. At least one single-entry-single-exit (SESE) region is identified based on the whole program representation. At least one node-specific SESE region is identified based on identified SESE regions and the at least one system parameter. Each node-specific SESE region is grouped into a node-specific subroutine. Each node-specific subroutine is compiled based on a specified node characteristic. The computer program code is modified based on the node-specific subroutines and the modified computer program code is compiled.