Cephalosporin is one of the best beta-lactam antibiotics, widely used in the treatment of infectious diseases. It is synthesized by Acremonium chrysogenum. The levels of cephalosporin produced by the improved strains obtained by classical mutation and selection procedures are still low compared to the penicillin titers obtained from the high-producing Penicillium chrysogenum strains. Most of the genes encoding the cephalosporin biosynthesis enzymes have been cloned, and some improvement of cephalosporin production has been achieved by removing bottlenecks in the pathway. One of the poorly-known steps involved in cephalosporin biosynthesis is the conversion of isopenicillin N into penicillin N catalyzed by the isopenicillin N epimerase system. This epimerization reaction is catalyzed by a two-component protein system encoded by the cefD1 and cefD2 genes that correspond, respectively, to an isopenicillinyl-CoA ligase and an isopenicillinyl-CoA epimerase. Comparative analysis of those proteins with others in the databanks provide evidence indicating that they are related to enzymes catalyzing the catabolism of toxic metabolites in animals. There are several biochemical mechanisms, reviewed in this article, for the biosynthesis of D-amino acids in secondary metabolites. The conversion of isopenicillin N to penicillin N in cephamycin-producing bacteria is mediated by a classical pyridoxal phosphate-dependent epimerase that is clearly different from the epimerization system existing in Acremonium chrysogenum. Modification of gene expression by directed manipulation of the cefD1-cefD2 bidirectional promoter region is a promising strategy for improving cephalosporin production. Improving our knowledge of the mechanism of epimerization systems is important if we wish to understand how microorganisms synthesize the high number of rare D-amino acids that are responsible, to a large extent, for the biological activities of many different secondary metabolites.