Regular observation of survival of the carp breeding lines constituting a living gene bank at the Institute of Ichthyobiology and Aquaculture in Golysz (Poland) over a period of at least 15 years showed different survival rates for various lines. In this study, we have examined the polymorphism of the major histocompatibility complex (MHC) gene class II B in nine carp lines. The class II B gene encodes for the part of the MHC class II molecule which presents peptides from pathogens and protein antigens that are present in the extracellular milieu and have been taken up into the endocytic vesicles of antigen-presenting cells. Polymerase chain reaction was used to amplify Cyca-DAB gene fragments comprising part of exon 1, complete intron 1 and almost complete exon 2. Exon 2 encodes for the β1 domain which is the most polymorphic fragment of MHC class II molecules. Single-strand conformational polymorphism (SSCP) was applied to detect different MHC class II B haplotypes. The analysis revealed the presence of seven different haplotypes occurring with various frequencies.