Neopterin concentrations reflect the activation of the cellular immune system. Neopterin is released by macrophages stimulated by interferon-γ (IFN-γ), which is produced by activated T lymphocytes. Raised neopterin concentrations in body fluids are found in various disorders, e.g. viral infections (AIDS, cytomegalovirus, hepatitis), intracellular bacteria infections (Mycobacteruim tuberculosis, Mycobacterium leprae), autoimmune disorders and malignancy. Neopterin concentrations are low or not significantly increased in bacterial infections, with exception of infections with intracellular bacteria. The aim of this study was to evaluate the usefulness of neopterin in the differential diagnosis of viral (Rotavirus) and bacterial (Salmonella) origin of diarrhoea. 129 children, aged 1 month -14 years, who were hospitalized for rotavirus gastroenteritis or salmonellosis were included into the study. Rotavirus was identified by latex test and Salmonella by stool cultures and the children were divided into 2 groups: with rotavirus infection (group I (R) -71 children) and with salmonellosis (group II (S) -58 children). In this study it was analyzed: disease duration before hospitalization, the general condition of a child on admission, body temperature, the number of loose and bloody stools and the number of vomits. On their admission to hospital, erythrocyte sedimentation rate (ESR), leukocyte count, and in the sera of all children C-reactive protein (CRP) and neopterin concentrations were determined. The serum neopterin concentrations were analyzed by ELISA. Mean neopterin concentration was 35.0 nmol/L in patients with salmonellosis, and it was significantly higher than in patients with rotavirus infection (22.0 nmol/L; p <0,001). The neopterin level that reliably discriminated between rotavirus diarrhoea and salmonellosis was 22 nmol/L: neopterin concentration higher than 22 nmol/L suggested diarrhoea caused by Salmonella, and neopterin concentrations equal or lower than 22 nmol/L suggested a rotavirus diarrhoea The combination of the results of two (neopterin >10 nmol/L and CRP >10mg/L) or three (neopterin >10nmol/L, ESR >10mm/h, CRP >10mg/L) serum markers helps to achieve better results. The best specificity (100%) was obtained for CRP concentration >15mg/L and neopterin concentration >37 nmol/L. We conclude that serum neopterin concentrations in children with acute diarrhea are not a laboratory indicator diversifying salmonellosis and rotavirus infection, because it increases in both infections. However higher concentrations indicate salmonellosis.