A cross-sectional study was undertaken to determine whether there was any association between intestinal infection (with parasites, cytomegalovirus, or Clostridium difficile) and clinical disease severity in patients with ulcerative colitis (UC). Consecutive cases of UC were enrolled after history and clinical examination, evaluated for presence of stool parasites (routine/special stains) and C. difficile toxins A and B (CDT) in stools. Segmental biopsies at colonoscopy were assessed for cytopathic changes of cytomegalovirus (CMV) infection. Statistical analysis was done to look for associations between the presence of infection and disease severity as assessed by the Truelove-Witts criteria. Eighty-seven patients (males = 51) of mean (SD) age 40.2 (12) years were enrolled. Thirty-nine patients (44.8 %) had severe disease, 11 (12.6 %) had moderate, and 37 (42.6 %) had mild disease. Ten (11.5 %) patients had parasites detected in stool, two (2.3%) had histological evidence of CMV, and three (3.4 %) were positive for CDT. The presence of pathogens was very significantly associated with moderate/severe UC. Thirteen of 15 cases (86 %) with detectable pathogens had moderate or severe UC compared to 37 of 72 cases (51 %) without detectable pathogens (p = 0.0194). The relative risk of a UC patient with stool pathogens having severe disease was 1.686 (95 % CI 1.250 to 2.276) compared to one without stool pathogens. The presence of stool pathogens was associated with disease severity in UC.