Major histocompatibility complex (MHC) proteins play a central role in the immune recognition of antigen. The generation of hybrid MHC molecules has been of great value in elucidating the structure: function relationships of these key glycoproteins. In this report, the generation of cDNAs coding for seven such hybrid proteins is described. We have used the technique of splicing by overlap extension by the polymerase chain reaction (SOE by PCR) [Horton, R.M., Hunt, H.D., Ho, S.N., Pullen, J.K. and Pease, L.R. (1989) Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 77, 61-68] to generate intermediate products of each of the components of the hybrid, tipped with a small sequence of the other, and then mixed these products in a second-stage PCR to produce the final spliced product. Where we were unable to generate final product, we introduced an additional step of asymmetric PCR synthesis to generate an excess of those strands which would anneal in the final PCR and found this to be effective. We noted a significant but manageable mutation rate, possibly contributed to by the tendency of DNA polymerase to add additional non-templated nucleotides [Hu, G. (1993) DNA polymerase-catalyzed addition of nontemplated extra nucleotides to the 3' end of a DNA fragment. DNA Cell Biol. 12, 763-770]. To avoid this, we modified our protocol to include a stage of blunting our intermediate products with T4 DNA polymerase prior to mixing them in the final PCR. We present this system as an effective mechanism to splice DNA.