Real time quantitative PCR (RQ-PCR) assays were developed for the measurement of differential real-time expression of immune-related genes in skin and whole blood from Cyprinus carpio during an infection with the ectoparasite Ichthyophthirius multifiliis. The target genes included the chemokines CXCa and CXCb, the chemokine receptors CXCR1 and CXCR2, the pro-inflammatory cytokines interleukin 1 beta (IL-1 beta) and tumour necrosis factor alpha (TNF-alpha) and the enzymes inducible nitric oxide synthase (NOS) and arginase 2. The strongest up-regulation in skin was observed in the IL-1 beta, CXCR1 and iNOS genes at 36-48 h post-exposure to theronts. A significant up-regulation of the genes CXCa and TNF-a was also observed. An up-regulation of the expression of the genes CXCa, CXCR1, IL-1 beta and iNOS was likewise found in blood, although the increase in the expression levels was more moderate and the expression peak was detected earlier in comparison with the skin. In addition, CXCR2 and the arginase 2 genes were specifically induced in blood. Our results confirm the role of CXCR1 and IL-1 beta as two prominent molecules involved in the initiation of the inflammatory process in fish in relation to an ectoparasite infection. Moreover, this study confirms the role of carp skin as an important source of pro-inflammatory molecules as well as an active modulator of the local inflammation. Finally, expression and regulation of the evaluated genes in blood confirm the important role of the migrated leucocytes in the immune response against I. multifiliis. (C) 2006 Elsevier Ltd. All rights reserved.