The major histocompatibility complex (MHC) plays an important role in regulation of the immune response. The MHC class I and II genes were selected as candidates to investigate associations with vaccine response to Salmonella enteritidis and kinetics of antibody response to sheep red blood cell (SRBC) and Brucella abortus. Primary antibody response after S. enteritidis vaccination at day 10, and antibody response to SRBC and killed B. abortus after immunization at 19 and 22 weeks were measured in an F2 population. The resource population was derived from males of two highly inbred MHC-congenic Fayoumi chicken lines (M5.1 and M15.2) mated with highly inbred G-B1 Leghorn line hens. Secondary phase parameters of minimum titers ( Y(min)), maximum titers ( Y(max)), and time needed to achieve Y(min) ( t(min)) and Y(max) ( t(max)) were estimated from post-secondary titers by using a non-linear regression model. Associations of single nucleotide polymorphisms (SNPs) in MHC class I and II genes with antibody response parameters were determined by a general linear model. Significant associations were found primarily in the M15.2 grandsire haplotype. There were significant associations between MHC class I alpha(1) and alpha(2) SNPs and antibody response to S. enteritidis, primary antibody response to B. abortus, Y(min) to SRBC, and Y(max) to both SRBC and B. abortus. There were significant effects of the MHC class II beta(1) domain SNP on S. enteritidis antibody and Y(max) to SRBC. The results suggest that the characterized SNPs might be used in future applications by marker-assisted selection to improve vaccine response and immunocompetence in chickens.