Cytokines and acute phase proteins (APP) are important mediators of the immune system and sensitive parameters to assess the immune status of mammals. Especially in newborn animals, maturation of the immune system is important for their survival. However, only little information is available for pinnipeds. To get baseline levels and investigate the development of the immune system, cytokine and APP expression was analysed in blood samples of six and eight harbour seal pups collected at the German North Sea Coast in 2004 and 2005, respectively. Blood samples were taken at admission and after rehabilitation in the Seal Centre Friedrichskoog. mRNA expressions of interleukin (IL)-1 beta, 2, 4, 6, 8, 10, 12, interferon (IFN)gamma, and transforming growth factor (TGF)beta, as well as of APP haptoglobin (HP), heat shock protein (HSP) 70 and metallothionein (MT) 2 were analyzed using real time RT-PCR. Cytokine and APP expression varied between animals and years. However, general changes during rehabilitation of pups were present. Higher levels of pro-inflammatory cytokines IL-1 beta, 6, 8, and 12 were found at admission, consistent with an activated immune system, whereas the anti-inflammatory cytokine IL-4 was increased after rehabilitation, suggesting recovery from infections and maturation of the immune system during rehabilitation. This preliminary study suggests that cytokines are sensitive parameters to assess the immune system of harbour seals.