A cross-sectional study of children in West Kalimantan, Indonesia, was conducted to examine the relationship between malnutrition history, child IQ, school attendance, socioeconomic status, parental education and parental IQ. In unadjusted analyses, severely stunted children had significantly lower IQ scores than mild-moderately stunted children. This effect was significant when stunting, school attendance and parental education were included in multivariable models but was attenuated when parental IQ was included. Our research underscores the importance of accounting for parental IQ as a critical covariate when modeling the association between childhood stunting and IQ.