Alloantigen genes B and C of respective loci Ea-B, the major histocompatibility complex (MHC) of chickens, and Ea-C were detected in Leghorn lines R and S selected from common ancestry for resistance and susceptibility to acute cecal coccidiosis, Eimeria tenella (ACC). The lines share genes B2 and C1; R line has B5, Br, and C4, and S line has B1, B3, B4, B6, C2, and C3. Haplotype Br is an apparent recombinant of B2 and B5, possibly F2G2-5. Expression of the F2G2- region of B2 and Br is strong in graft-vs.-host reactions but weak on erythrocytes; in contrast, that of F5G5- of B5 is reduced in graft-vs.-host reactions but strong on erythrocytes. Extinction of B4 in R line and B5 in S line occurred in the last stages of selection, and the frequency of B5 in R line increased as a result of intensification of selection pressure for resistance to coccidiosis. The respective C genes of highest frequency in lines R and S are C1 and C3. The latter is a probable recombinant of C1 and C2. Evidence of roles of the B and C systems in resistance and previous similar evidence for the AE system indicates that genes other than the chicken MHC have measurable effects on infectious diseases.