The objective of the present study was to investigate the inter-relationships between nutritional status (past and current nutrition), brain development, and scholastic achievement (SA) of Chilean high-school graduates from high and low intellectual quotient (IQ) and socio-economic status (SES) (mean age 18·0 (SD 0·9) years). Results showed that independently of SES, high-school graduates with similar IQ have similar nutritional, brain development and SA variables. Multiple regression analysis between child IQ (dependent variable) and age, sex, SES, brain volume (BV), undernutrition during the first year of life, paternal and maternal IQ (independent variables) revealed that maternal IQ (P<0·0001), BV (P<0·0387) and severe undernutrition during the first year of life (P<0·0486), were the independent variables with the greatest explanatory power for child IQ variance (r2 0·707), without interaction with age, sex or SES. Child IQ (P<0·0001) was the only independent variable that explained both SA variance (r2 0·848) and academic aptitude test variance (r2 0·876) without interaction with age, sex or SES. These results confirm the hypotheses formulated for this study that: (1) independently of SES, high-school graduates with similar IQ have similar variables of nutritional status, brain development and SA; (2) past nutritional status, brain development, child IQ and SA are strongly and significantly inter-related. These findings are relevant in explaining the complex interactions between variables that affect IQ and SA and can be useful for nutritional and educational planning.