Inflammatory processes are known to take place in the skin of fish during an infection with the parasitic ciliate Ichthyophthirius multifiliis. The present study shows that the pro-inflammatory cytokines interleukin 1 beta (IL-1β) and tumor necrosis factor alpha (TNF-α), the chemokine interleukin 8 (IL-8) and the type II IL-1 receptor (IL-1RII) are expressed in rainbow trout during an infection. In the skin an up to 17.8 times increase in the expression level of IL-1β relative to uninfected controls was seen 4 days after infection. Upregulated expression of IL-1β was likewise observed in the head kidney and spleen during the infection although to a lesser degree. TNF-α expression was seen in all examined tissues, with an increase in transcript level in the skin of up to 3.2 times the level in uninfected fish. A significant increase in the expression of IL-8 was evident in the skin and also to a lower extent in the head kidney and spleen. Expression of the down regulatory IL-1RII was seen in all three tissues. The potential involvement of the expression of these genes and their relevance in an infection with I. multifiliis are discussed.