Dietary levels of n-3 PUFA are believed to influence the immune system. The importance of the source of n-3 PUFA is debated. This study addressed how the content and source of n-3 PUFA in the maternal diet influenced tissue FA composition and the immune response to ovalbumin (OVA) in mice pups. From the day of conception and throughout lactation, dams were fed diets containing 4% fat from linseed oil (LSO), fish oil (FO) or a n-3 PUFA-deficient diet (DEF). Pups were injected with OVA within 24 h of birth and sacrificed at weaning (day 21). Overall, the content of n-3 PUFA in milk, liver and spleen reflected the source and only minor differences were observed in brain phospholipid 22:6n-3. The source had only limited influence on the n-3 PUFA accretion in peripheral tissue, with most pronounced differences in the spleen. The marine PUFA-group had reduced levels of total OVA-specific antibodies and OVA-IgG1 titers in the pup blood, while the response in the LSO-group did not differ from that in the DEF-group. There were no statistical differences in the cytokine responses to OVA-stimulated splenocytes, but the decrease in IgG1 was paralleled by an increase in IFNγ-production and a decrease in IL-6-production. Our results indicate that maternal intake of FO, but not of LSO, changes the offspring’s antigen-specific response and potentially increases Th1-polarization.