Although human infection with Ascaris appears to be associated with protection from cerebral malaria, there are many potential socio-economic and nutritional confounders related to helminth infection that need to be considered. In a hospital-based study, 37 cases of cerebral malaria and 61 cases of non-severe malaria with high parasite biomass (i.e. hyperparasitaemia and/or circulating schizonts) answered a structured questionnaire and were screened for intestinal helminths. Logistic regression was then used to adjust for the potential confounders. The adjusted odds ratios (OR) and their 95% confidence intervals (CI) still showed a significant protective association for helminths (OR = 0.24; CI = 0.07-0.78, P = 0.02) and malnutrition (OR = 0.11; CI = 0.02-0.58; P = 0.01), with no evidence of interaction between the two. There was also a significant dose-effect trend for the helminth infections (P = 0.048). These results, despite coming from a hospital-based study, indicate that the apparent association between helminths and protection from cerebral malaria is not the result of socio-economic or nutritional confounders.