Co-infection by intestinal helminths and Plasmodium spp. may be common in endemic communities. Several studies have identified a relationship between helminth infection, Plasmodium spp. infection and malaria severity. However, the relationship is not well defined, and results are inconclusive. We analyzed 202 stool samples from a cohort of children with severe malaria enrolled in two hospitals in Uganda from 2014-2017 and asymptomatic community children from the same household or neighborhood and enrolled at the same time, all 6 months to 48 months of age. We investigated if intestinal helminth infection modified risk of severe malaria. We extracted nucleic acids from stool and tested them for six helminth species (Anyclostoma duodenale, Ascaris lumbricoides, Necator americanus, Strongyloides stercolaris, Trichuris trichiura, Shistosoma mansoni) using highly sensitive quantitative PCR. We found a low prevalence of infection by ≥1 intestinal helminth species in children with severe malaria (5.1%, n=9/177) and community control children (4.0%, n=1/25). Infection by ≥1 of the helminths assessed was not associated with severe malaria (aRR = 1.0, 95% Confidence Interval = 0.82, 1.3, p = 0.78). In 2003 Uganda instituted a national deworming program, with anti-helminth medication provided twice annually to children 6 months to 5 years of age. In these areas of Uganda, the national deworming campaign has been highly successful, as stool-based helminth infection was rare even when using highly sensitive methods of detection and was not a major contributor to risk of severe malaria.