Genes of the major histocompatibility complex (MHC) are crucial elements of adaptive immunity. High polymorphism renders the MHC genes highly suitable for studies on association with disease resistance. In common carp (Cyprinus carpio L.), there are two paralogous groups of MH class II B genes, Cyca-DAB1-like and Cyca-DAB3-like genes. The Cyca-DAB1-like genes especially, could be linked to high polymorphism and increased antibody responsiveness. The aim of the present study was to analyze the association between Cyca-DAB1-like genotypes, as revealed by polymerase chain reaction — restriction fragments — single strand conformation polymorphism (PCR-RF-SSCP), and disease resistance. We used a large number of individuals of different genetic background and performed standardized disease challenges with the bacterium Aeromonas hydrophila, the ectoparasite Argulus japonicus, and the blood parasite Trypanoplasma borreli. Genotyping revealed the presence of n = 9 unique Cyca-DAB1-like genotypes, of which three genotypes (B, D, and E) were most common. We could detect significant associations between genotype E and low level of A. japonicus and between genotype D and higher level of parasitaemia after T. borreli infection. The Cyca-DAB1-like group of genes comprises (at least) two gene copies, Cyca-DAB1 and Cyca-DAB2. We observed a significant association between Cyca-DAB1 heterozygosity and lower level of parasitaemia after T. borreli infection. Cyca-DAB2 was often homozygous or absent. Our data suggest that Cyca-DAB1 allelic polymorphism can be used as potential genetic markers in future breeding programs of common carp.