In the past few years the DNA sequence database for molecules of the MHC (major histocompatibility complex) has expanded greatly, yielding a more complete picture of the long-term rates and patterns of evolution of the MHC in vertebrates. Sharing of MHC allelic lineages between long-diverged species (trans-species evolution) has been detected virtually wherever it is sought, but new analyses of linked neutral regions and the complexities of sequence convergence and microrecombination in the peptide binding region challenge traditional phylogenetic analyses. Methods for estimating the intensity of selection on MHC genes suggest that viability is important, but recent studies in natural populations of mammals give inconsistent results concerning mate choice. The complex and interacting roles of microrecombination, parasite-mediated selection and mating preferences for maintaining the extraordinary levels of MHC polymorphism observed are still difficult to evaluate.