In recent years, a number of gene clusters involved in the biosynthesis of polyketide compounds have been characterized and the genes have been used for designing and developing novel chemical entities by combinatorial biosynthesis. This review covers the highlights of combinatorial biosynthesis using polyketide-modifying enzymes such as oxidoreductases, group transferases, halogenases, cyclases and deoxysugar biosynthesis enzymes, focusing on those from actinomycetes (with 315 references cited).