Embedded Cartesian Genetic Programming (ECGP) is an extension of Cartesian Genetic Programming (CGP) that can automatically acquire, evolve and re-use partial solutions in the form of modules. In this paper, we introduce for the first time a new multi-chromosome approach to CGP and ECGP that allows difficult problems with multiple outputs to be broken down into many smaller, simpler problems with single outputs, whilst still encoding the entire solution in a single genotype. We also propose a multi-chromosome evolutionary strategy which selects the best chromosomes from the entire population to form the new fittest individual, which may not have been present in the population. The multi-chromosome approach to CGP and ECGP is tested on a number of multiple output digital circuits. Computational Effort figures are calculated for each problem and compared against those for CGP and ECGP. The results indicate that the use of multiple chromosomes in both CGP and ECGP provide a significant p...