During the last decade, the major histocompatibility complex (MHC) has received much attention in the fields of evolutionary and conservation biology because of its potential implications in many biological processes. New insights into the gene structure and evolution of MHC genes can be gained through study of additional lineages of birds not yet investigated at the genomic level. In this study, we characterized MHC class II B genes in five families of birds of prey (Accipitridae, Pandionidae, Strigidae, Tytonidae, and Falconidae). Using PCR approaches, we isolated genomic MHC sequences up to 1300 bp spanning exons 1 to 3 in 26 representatives of each raptor lineage, finding no stop codons or frameshift mutations in any coding region. A survey of diversity across the entirety of exon 2 in the lesser kestrel Falco naumanni reported 26 alleles in 21 individuals. Bayesian analysis revealed 21 positively selected amino acid sites, which suggests that the MHC genes described here are functional and probably expressed. Finally, through interlocus comparisons and phylogenetic analysis, we also discuss genetic evidence for concerted and transspecies evolution in the raptor MHC.