Protozoa contain thymidylate synthase (TS) and dihydrofolate reductase (DHFR) on the same polypeptide. In the bifunctional protein, the DHFR domain is on the amino terminus, TS is on the carboxyl terminus, and the two domains are separated by a junction peptide of varying size depending on the source. The native protein is composed of a dimer of two such subunits and is 110-140 kDa. Most studies of the bifunctional TS-DHFR have been performed with the protein from anti-folate resistant strains of Leishmania major, which show amplification of the TS-DHFR gene and overproduction of the bifunctional protein. The Leishmania TS-DHFR has also been highly expressed in heterologous systems. There appears to be extensive communication among domains and channeling of the H2folate product of TS to DHFR. Anti-folates commonly used to treat microbial infections are poor inhibitors of L. major DHFR. However, selective inhibition of L. major vs. human DHFR does not appear difficult to achieve, and selective inhibitors are known. The TS-DHFR from Plasmodium falciparum has also been cloned and has recently been expressed in Escherichia coli, albeit in small amounts. Interestingly, pyrimethamine-resistant strains of P. falciparum all have a common point mutation in the DHFR coding sequence (Thr/Ser 108 to Asn), which causes decreased binding of the folate analog. It is suggested that if an appropriate inhibitor of the pyrimethamine-resistant P. falciparum DHFRs can be found, it may serve in combination with pyrimethamine as an antimalarial regimen with low propensity for the development of resistance. In the future, we project that we will have a detailed knowledge of the structure and function of TS-DHFRs, and have the essential tools necessary for a molecular-based approach to drug design.