Genetic variation within exon 2 of chicken major histocompatibility complex B-LB // genes was investigated by PCR amplification, cloning and sequencing of a 374 bp fragment of the indigenous Tibetan chicken genomic DNA. Fifteen novel B-LB // alleles were found. Alignment and comparison of 18 allelic sequences from the individuals sampled revealed a total of 62 variable sites (total of 80 mutations) in exon 2, of which 41 were parsimony informative sites. The nucleotide diversity (pi) within the sequence of exon 2 was calculated to be 0.0718. Analysis of nucleotide variation confirmed a lower level of divergence (0.056 +/- 0.008) as estimated by average pairwise distance within the Tibetan chicken population than the five exotic breeds detected. The relative frequencies of synonymous and non-synonymous nucleotide substitutions within the region were 3.25 +/- 0.94% and 15.61 +/- 2.69% , respectively. These results indicated that the genetic variation within exon 2 seemed to have arisen largely by gene recombination and balancing selection. Alignment of the deduced amino acid sequences of beta1 domain coded by exon 2 revealed 11 synonymous mutations and 27 non-synonymous substitutions at the 38 separate sites. Fifty percent (12/24) of the proposed peptide-binding sites were variable within beta1 domain of chicken MHC B-LB // molecules, of which 11 were unique non-synonymous amino acid substitutions. These particular non-synonymous substitutions are considered to be associated with immunological specificity of MHC B-LB // molecule in Tibetan chicken, and they can provide a molecular biological basis for the study of disease resistance in chicken.