Background Little information exists about the relationship of nutritional status and motor performance conditional on asymptomatic parasitemia in rural African children. Aims The aims of this study were to (1) determine if malnourished youths from rural African areas have lower levels of physical fitness (PF) and physical activity (PA) compared to normal weight youths, (2) verify the biological relevance of anthropometric criteria used to classify nutritional status in youth, and (3) determine the prevalence of parasitological indicators, and its association with nutritional status and PF. Methods The sample comprised 794 youths (6–17 years) from Calanga, a rural community in Mozambique. PF tests were selected from standardized test batteries, and PA was estimated by accelerometry. Nutritional status was defined according to WHO recommendations for stunting, wasting and normal weight. Parasitological indicators were determined based on stool specimens' analysis. Results In general terms the normal group out‐performed the other nutritional groups (stunted and wasted) for PF. However, no significant differences were found for PA among nutritional groups. There were also no significant differences in prevalence of intestinal parasites. Conclusions Nutritional status was not associated with PA levels or the prevalence of parasitological indicators in youth, but was related to physical performance. Am. J. Hum. Biol. 25:516–523, 2013. © 2013 Wiley Periodicals, Inc.