The immune system plays an important role in protecting poultry from diseases. Understanding genetic control of immune response can be utilized to improve chicken health. Adult F2 hens were generated by mating highly inbred males of two MHC-congenic Fayoumi lines with G-B1 Leghorn hens. Antibody response after Salmonella enteritidis (SE) vaccination at day 10, and sheep erythrocyte (SRBC) and killed Brucella abortus (BA) immunizations at 19 and 22 weeks were measured. Agglutinating antibody titer at 7 day after primary immunization and mean titer of the final three samples (day 18, 32, and 63 after 2nd immunization) were used as parameters for primary and equilibrium phases, respectively. Secondary phase parameters of minimum (Ymin), maximum titers (Ymax) and time needed to achieve minimum (Tmin) and maximum (Tmax) titers were estimated from seven post-secondary titers using a nonlinear regression model. Both candidate gene and genome scan approaches were used to identify quantitative trait loci (QTL) affecting antibody response to SE vaccination and antibody response kinetics to SRBC and BA. Using the genome scan approach, QTL affecting immune response to SRBC and BA were detected by a stepwise process that culminated in interval mapping. Five significant QTL were detected at the 5% chromosome-wise level on chicken chromosomes 3, 5, 6 and Z, suggesting that regions on chromosomes 3, 5, 6 and Z contain QTL affecting antibody kinetics to SRBC and BA. Single nucleotide polymorphisms (SNP) of 15 immunity related genes were identified. Interferon-gamma, immunoglobulin light chain, interleukin-2, MHC class I alpha1, alpha2, class II beta1, and transforming growth factor-beta 2, 3 and 4 SNP were significantly associated with antibody responses to SE vaccination or antibody response kinetics to SRBC and BA or both. For some candidate genes, significant associations were primarily detected in the lineage of the M5.1 grandsire, but in that of the M15.2 grandsire on the others. Strong interactions of the MHC with candidate genes on antibody response were indicated from the study. All the genes characterized in the present study are, therefore, strong potential candidates for application in marker-assisted selection to improve vaccine response and immunocompetence in chickens.