Background: Chronic malnutrition during infancy, marked by stunting, has been associated with poor cognitive function. We assessed the effect of stunting, diarrhoeal disease, and parasitic infections during infancy on cognitive function in late childhood. Methods: We followed up from birth to 2 years, a cohort of 239 Peruvian children for anthropometrics, stool samples, and diarrhoeal status. At 9 years of age, we assessed cognitive function in 143 (69%) with the full-scale intelligence quotient of the Wechsler intelligence scale for children-revised (WISC-R). Findings: All findings were adjusted for socioeconomic status and schooling; in addition, findings related to diarrhoea prevalence, Giardia lamblia, and Cryptosporidium parvum were adjusted for severe stunting. During the first 2 years of life, 46 (32%) of 143 children were stunted. Children with severe stunting in the second year of life scored 10 points lower on the WISC-R test (95% CI 2.4-17.5) than children without severe stunting. Children with more than one episode of G lamblia per year scored 4.1 points (0.2-8.0) lower than children with one episode or fewer per year. Neither diarrhoea prevalence nor Cparvum infection was associated with WISC-R scores. Interpretation: Malnutrition in early childhood, indexed by stunting, and potentially G lamblia, are associated with poor cognitive function at age 9 years. If the observed associations are causal, then intervention programmes designed to prevent malnutrition and G lamblia early in life could lead to significant improvement in cognitive function of children in similar lower-income communities throughout the less-developed world.