A randomized clinical trial was carried out to compare a locally available maize-cowpea-palm oil diet (group MCP) with a commercially produced lactose-free, soy protein isolate formula (group SF) for the dietary management of 69 Nigerian boys, 6-24 months of age, hospitalized for acute, watery diarrhea. Although the treatment groups were generally similar initially, the children in group SF had slightly lower mean weight-for-age z scores (p = 0.08), lower serum bicarbonate levels (p = 0.04) and greater stool outputs during the period of rehydration before the diets were initiated (p = 0.01). Rates of treatment failure in group MCP (5.7%) and group SF (8.8%) were similar (p = 0.67). There were no significant differences in the adjusted mean stool outputs by study group on days 1-5, but the children in group SF had slightly lower fecal weights on day 6 (p = 0.05). Children in group MCP had a substantially reduced duration of liquid stool excretion (estimated median duration 42 h versus 140 h; p < 0.001). On the other hand, children in group SF consumed considerably more of their diet, had greater net absorption of macronutrients and greater rates of weight gain than those in group MCP. We conclude that children can safely consume the MCP diet during acute, watery diarrhea without increasing their risk of treatment failure or augmenting stool output. However, the diet may not be adequate as a sole source of nutrients beyond the period of acute illness.