A real time quantitative PCR (RQ-PCR) assay was developed for measurement of differential expression of the genes encoding the acute phase reactant serum amyloid A (SAA), transferrin (TF) and a C-type lectin molecule (CL) in skin, blood and liver from Cyprinus carpio following infection with the ectoparasite Ichthyophthirius multifiliis. Serum amyloid A and CL were constitutively expressed in all organs evaluated while TF transcripts were only detected in the liver. A dramatic up-regulation (1600 times) in the expression levels of SAA was observed in skin 36 h after the parasite infection. A similar increase in the number of RNA molecules encoding for SAA was observed in the liver. The CL expression was significantly down regulated in all the organs and no significant change was observed in the expression levels of the TF in the liver. These results indicate that SAA plays a major role in the acute phase response in fish infected with I. multifiliis and emphasize the importance of the fish skin as an active organ in response to an ectoparasite infection.