Cytokines are important cell mediators involved in immune responses. Their expression can be modulated by numerous factors, including stress. The aim of this study was to compare cytokine mRNA expression from harbour porpoises exposed to different environments. Blood samples were taken from two healthy porpoises living in captivity at the Fjord and Belt Centre Kerteminde, Denmark, and from four wild porpoises accidentally caught in Danish waters. Real-time RT-PCR was used to quantify the transcription of interleukin-(IL)-1β, IL-2, -4, -6, -10, tumour necrosis factor-(TNF)-α, transforming growth factor-(TGF)-β and the acute phase protein haptoglobin. This revealed downregulation of the pro-inflammatory cytokines IL-1β, IL-2, IL-6 and TNFα, and a switch towards the T-helper-cell-(Th)2- and Th3-cytokines, IL-4 and TGFβ, in blood samples of the wild-captured animals. This indicated a shift towards immunomodulatory cytokines. In addition, cortisol levels were increased in the wild-caught porpoises. These results are suggestive of stress-induced modulation of the immune responses in the accidentally caught animals. The current study indicates that the expression pattern of these cytokines and the estimation of the Th1- to Th2- and Th3-cytokine mRNA ratios might be a useful indicator to analyse the influence of stress on the immune system in harbour porpoises.