Harbor porpoises from the North and Baltic Seas exhibit a higher incidence of bacterial infections compared to whales from less polluted arctic waters. Toxicological analysis revealed an association between elevated body burdens of environmental contaminants, such as polychlorinated biphenyls (PCB) and polybrominated diphenyl ether (PBDE) and lymphoid depletion in thymus and spleen of these whales. However, it remains undetermined if changes in the immune system are primarily contaminant-induced or a sequel of infectious diseases and emaciation. The aim of the present study was to investigate changes of blood cytokine mRNA levels in healthy and diseased harbor porpoises. Therefore, 29 by-caught and stranded whales were necropsied and the health status was evaluated based upon main pathological findings. Furthermore, the degree of thymic atrophy and splenic depletion was histologically graded using a semi-quantitative scoring system. Gene expression of interleukin (IL)-2, IL-4, IL-6, IL-10, transforming growth factor-β and tumor necrosis factor-α in the blood was measured by real time reverse transcription-polymerase chain reaction. Thymic atrophy and splenic depletion were correlated with an impairment of the animals’ health status. Additionally, a marked up-regulation of IL-10 was predominately found in severely diseased whales with evidence of chronic bacterial infections. Furthermore, increased IL-10 levels were associated with splenic depletion. Other investigated cytokines were not significantly associated with the health status or lymphoid depletion, respectively. The present study indicated that lymphoid depletion represents a sequel of chronic infectious diseases in a portion of investigated harbor porpoises. Regarding this, expression of anti-inflammatory cytokines, such as IL-10 might represent a consequence of continuous stimulation of the immune system and induction of immunomodulatory mechanisms in this cetacean species.