In animal studies, glutamine (Gln) reduces chemotherapy-associated mucositis and mucosal atrophy. Therefore, this study examined the protective effects of a parenteral Gln supplementation in patients with metastatic colorectal carcinoma receiving 5-fluorouracil (5-FU)/calcium-folinate (CF) chemotherapy. In a prospective study, a total of 24 patients underwent three courses of 5-FU/CF chemotherapy and were randomised with (n = 12) or without (n = 12) glycyl-L-glutamine. Effects on gastrointestinal mucosa were assessed by endoscopic examinations and histomorphometric measurements. Clinical side-effects were documented according to the World Health Organisation grading. In the Gln group, a significant reduction in mucositis and ulcerations of the gastric (P < 0.01) and duodenal mucosa (P < 0.05) was documented after the third course of chemotherapy. In the same group, the villus height/crypt depth ratio was significantly higher after therapy than in the unsupplemented group (1st course P < 0.01; 3rd course P < 0.05). However, there were no significant differences in the incidence and severity of clinical side-effects. The results suggest that parenteral Gln supplementation protects the gastrointestinal mucosa against 5-FU/CF chemotherapy-induced damage.