Expression of immune-regulatory genes that code for cyclooxigenase-2 (COX-2), transforming growth factor beta (TGF-beta), and two isoforms of interleukin-1beta (IL-1beta1 and IL-1beta2) was studied in susceptible and non-susceptible rainbow trout strains for 200 days after exposure to Myxobolus cerebralis. Expression of COX-2, IL-1beta1, and IL-1beta2 increased 5 min post exposure (p.e.) and was always more elevated in the susceptible strain than in the non-susceptible strain. In both strains, expression of COX-2 returned to the control level within a few hours p.e. Expression of IL-1beta1 and IL-1beta2 showed two elevated waves in both strains until 4 days p.e. Expression of TGF-beta in the non-susceptible strain was elevated at nearly all sampling points, but was decreased in the susceptible strain until up-regulation between 4 and 20 days p.e.; TGF-beta was the only gene where the expression in the non-susceptible strain was more elevated than in the susceptible strain. Rainbow trout of the non-susceptible strain appeared to resist infection by M. cerebralis with only minor transcriptional regulation of the genes investigated. Increased transcriptions of genes in the susceptible strain may be the result of an inability to antagonize the infection.