The purpose of this study was to determine if cytokine production in intestinal and mesenteric lymph node tissue of cattle naturally infected with M. paratuberculosis reflects a Th1-type pattern in early disease and a Th2 pattern in advanced infection. The experimental approach was to measure cytokine mRNA in tissues harvested at slaughter, using a reverse-transcriptase, competitive polymerase chain reaction (RT-cPCR) assay. Eleven adult Holstein cows (from 7 herds) infected with M. paratuberculosis were identified by fecal culturing. Four of the cows had clinical signs of paratuberculosis (diarrhea, weight loss) and 7 of the infected cows were asymptomatic. Samples were also obtained from 5 uninfected herd mates of the infected cows. At the time of slaughter, samples of ileum and ileocecal lymph node were frozen in liquid nitrogen immediately after collection, and stored at 70^oC until RT-cPCR was performed. For ileum and mesenteric lymph node samples, the IFN-gamma mRNA concentration was highest in the asymptomatic infected group, approximately 3 fold higher than the control and clinically affected cows. The difference between the asymptomatic group and the control and clinically affected groups was significant. No significant difference was detected in IL-4 mRNA concentration in intestinal tissue nor mesenteric lymph node, although there was a trend towards higher IL-4 concentration in the clinically affected cows. These data support the hypothesis that progression of infection to the clinical stage is associated with a reduced Th1 response.