Toll-like receptors (TLRs) play a crucial role in the innate immune system, but to date the roles of fish TLRs in response to parasitic infection are still poorly understood. In the present study, we used channel catfish (Ictalurus punctatus) and the ciliate parasite Ichthyophthirius multifiliis as a model to investigate whether and which fish TLRs play important roles in the immune response against parasitic pathogens by detecting the expression profiles of a complete set of TLRs in catfish at different time points after infection with I. multifiliis. The expression profiles of TLR1 and TLR2 were similar, and both were significantly up-regulated in the skin and head kidney at most time points after infection. Furthermore, the expression of TLR2 was also up-regulated in the gill and spleen. TLR9 was induced in the skin and gill, whereas TLR21 was induced in the head kidney and spleen after infection. For TLR19, significant up-regulation was observed in the skin and gill, but significant down-regulation was detected in the head kidney and spleen. In contrast to TLR19, TLR25 was significantly up-regulated in the head kidney and spleen at some time points. No significant changes were observed for the rest of the TLRs at most time points. The results indicated that some TLRs may play essential roles in catfish defense against I. multifiliis infection.