The major histocompatibility complex (MHC) is a family of genes coding for molecules which play important roles in the immune response as well as many other cellular processes of a vertebrate organism. The understanding of the immune system of some of the domestic animals will have both practical value and theoretical significance. The purpose of this work was to study the MHC of the chicken (B) and the swine (SLA). First, in order to study the MHC class II gene structure of the chicken, a genomic library was constructed from an inbred chicken line G-B2 (MHC haplotype B[superscript]6) and screened with a chicken class II probe ([beta]2 exon specific). Three MHC class II [beta] chain genomic clones were isolated. The restriction maps of the three clones showed that each of the three clones was unique. The position of the [beta] chain sequences was located in each of the three genomic clones by Southern blot hybridization. Subclones containing the [beta] chain gene were produced from each of the genomic clones and the orientation of LP, [beta]1, [beta]2, TM, CYT, and 3[superscript]'UT was determined by Southern blot hybridization and nucleotide sequencing. The complete nucleotide sequence of two of the three subclones was determined. Comparison of the nucleotide and predicted amino acid sequences of the two subclones with class II [beta] chain sequences from other chickens, human, and mouse showed that the B[superscript]6 chicken [beta] chain genes are evolutionarily related to the class II [beta] chain genes from chickens of other MHC haplotypes, and to the class II [beta] chain genes from other species. Analysis of the three MHC class II [beta] chain genes suggests that chickens of the B[superscript]6 haplotype possess at least three MHC class II [beta] chain genes. Second, the order of the genes in the SLA was determined by using pulsed field gel electrophoresis (PFGE). After genomic DNA from NIH miniature pigs was prepared with a molecular weight larger than 1 Mb, the DNA was digested with restriction enzymes, and then separated by PFGE. Southern blotting and hybridization were performed using SLA class I and class II probes, as well as human MHC class III probes. The autoradiogram patterns from the different probes were analyzed and the genes of the SLA complex were put in order on the chromosome: Centromere-class II-class III-class I. This order is the same as the order in mouse and human, indicating that the order of the MHC genes is conserved.