The relationship between genetic variation in major histocompatibility complex (MHC) Class I and II genes and susceptibility to sea lice Lepeophtheirus salmonis (Krøyer) in Atlantic salmon Salmo salar (L.) was studied in cage-reared post smolts. Polymorphic repeat markers located in the 3’ untranslated regions (3UTR) of the genes Sasa-UBA (MHC Class I) and Sasa-DAA (MHC Class II) were screened in 1004 fish sampled from 11 full-sibling families. This gave rise to a total of 7 and 5 alleles, and 17 and 13 genotypes respectively. Significant relationships between both Sasa-UBA-3UTR and Sasa-DAA-3UTR genotypes and abundance of lice were observed within the pooled material, within individual families, and within the pooled material with both markers combined. However, most of these associations were either weak, linked with variation in fish size among genotypes, or influenced by family background genome. Nevertheless, within one family, the Sasa-DAA-3UTR 248/278 genotype displayed a significantly higher (33%) abundance of lice compared with the Sasa- DAA-3UTR 208/258 genotype, and this difference was not influenced by fish size. Consequently, the results of this study indicate a link between MHC Class II and susceptibility to lice.