Deoxynivalenol is also known as vomitoxin due to its impact on livestock through interference with animal growth and acceptance of feed. At the molecular level, deoxynivalenol disrupts normal cell function by inhibiting protein synthesis via binding to the ribosome and by activating critical cellular kinases involved in signal transduction related to proliferation, differentiation and apoptosis. Because of concerns related to deoxynivalenol, the United States FDA has instituted advisory levels of 5 µg/g for grain products for most animal feeds and 10 µg/g for grain products for cattle feed. The aim of the study was to determine the effect of low doses of deoxynivalenol applied per os on the presence of this mycotoxin in selected tissues of the alimentary canal of gilts. The study was performed on 39 animals divided into two groups (control, C; n = 21 and experimental, E; n = 18), of 20 kg body weight at the beginning of the experiment. Gilts received the toxin in doses of 12 µg/kg b.w./day (experimental group) or placebo (control group) over a period of 42 days. Three animals from two experimental groups were sacrificed on days 1, 7, 14, 21, 28, 35 and 42, excluding day 1 when only three control group animals were scarified. Tissues samples were prepared for high performance liquid chromatography (HPLC) analyses with the application of solid phase extraction (SPE). The results show that deoxynivalenol doses used in our study, even when applied for a short period, resulted in its presence in gastrointestinal tissues. The highest concentrations of deoxynivalenol reported in small intestine samples ranged from 7.2 (in the duodenum) to 18.6 ng/g (in the ileum) and in large intestine samples from 1.8 (in transverse the colon) to 23.0 ng/g (in the caecum). In liver tissues, the deoxynivalenol contents ranged from 6.7 to 8.8 ng/g.