Early-life conditions influence organ growth patterns and their functions, as well as subsequent risk for non-communicable chronic diseases in later life. A limited number of studies have determined that in Bangladesh, kidney size relates to its function among children as a consequence of the maternal and postnatal conditions. The present study objectives were to determine early-life conditions in relation to childhood kidney size and to compare their influences on kidney function. The study was embedded in a population-based prospective cohort of 1067 full-term singleton live births followed from fetal life onward. Kidney volume was measured by ultrasound in children at the age of 4.5 years (range 45–64 months), and the estimated glomerular filtration rate (eGFR) was assessed at the age of 9 years (range 96–116 months). The mean (s.d.) kidney volume of children at 4.5 years was 64.2 (11.3) cm3, with a significant mean difference observed between low birth weight and normal birth weight children (P<0.001). The multivariable model showed, changes in status from low birth weight to normal birth weight children, with kidney volume increases of 2.92 cm3/m2, after adjusting for the child’s age, sex, maternal age and early pregnancy body mass index, and socio-economic index variables. One-unit change in kidney volume (cm3/m2) improved the eGFR to 0.18 ml/min/1.73 m2. The eGFR in low birth weight children was 5.44 ml/min/1.73 m2 less than that in normal birth weight children after adjustments. Low birth weight leads to adverse effects on kidney size and function in children.