Coccidiosis is a protozoan disease characterized by acute or chronic diarrhea in lambs and kids. It causes important economical losses. The disease is generally seen in young animals and may result in death because of the hemorrhagic enteritis. Inflammatory mediators play an important role in the pathogenicity of the disease. Numerous studies are available on the serum activities of cytokines, chemokines and acute phase proteins that provide important knowledge about the pathogenesis of the disease. In this study coccidiosis was examined clinically, parasitologically, cytologically, pathologically and immunohistochemically in lambs and kids. This study showed a relation between oocyst count and severity of cytological or histopathological findings. Lesions were generally localized in the small intestines, especially in the villus epithelium. The cytokine reaction at the gut lesions was examined by immunohistochemical methods. Marked increases were observed in all of the examined cytokine and chemokines. The most abundant expression was observed in interleukin-1 alpha and interferon-gamma, followed by interleukin-10, interleukin-1 beta, tumor necrosis factor-alpha, tumor necrosis factor-beta, interferon-alpha, interleukin-6 and interleukin-2. This study indicates that cytokines and chemokines play an important role and may be used for therapeutic or prophylactic purposes in coccidiosis. (C) 2011 Elsevier B.V. All rights reserved.