BackgroundGrowth patterns may be indicative of underlying changes in body composition. However, few studies have assessed the association of growth and body composition in poorly resourced regions experiencing the double-burden of malnutrition exists. Thus, the aims of this study were to investigate the association of intrauterine and postnatal growth patterns with infant body composition at 2 years in a middle-income country.MethodsParticipants were from the International Atomic Energy Agency Multicentre Body Composition Reference study. Fat mass (FM), fat free mass (FFM), Fat mass index (FMI), fat free mass index (FFMI), and percentage fat mass (%FM) were measured in 113 infants (56 boys and 57 girls), from Soweto, South Africa, using deuterium dilution from 3 to 24 months. Birthweight categories were classified using the INTERGROWTH-21 standards as small (SGA), appropriate (AGA), and large-for gestational age (LGA). Stunting (> -2 SDS) was defined using the WHO child growth standards. Birthweight z-score, conditional relative weight and conditional length at 12 and 24 mo were regressed on body composition at 24 mo.ResultsThere were no sex differences in FM, FFM, FMI and FFMI between 3 and 24 mo. SGA and AGA both had significantly higher %FM than LGA at 12 mo. LGA had higher FM at 24 mo. Children with stunting had lower FM (Mean = 1.94, 95% CI; 1.63–2.31) and FFM (Mean = 5.91, 95% CI; 5.58–6.26) at 12 mo than non-stunting, while the reverse was true for FFMI (Mean = 13.3, 95% CI; 12.5–14.2) at 6 mo. Birthweight and conditionals explained over 70% of the variance in FM. CRW at both 12 and 24 mo was positively associated with FM and FMI. CRW at 12 mo was also positively associated with FMI, while CH at 24 mo was negatively associated with both FFMI and FMI in boys.ConclusionBoth LGA and SGA were associated with higher body fat suggesting that both are disadvantaged nutritional states, likely to increase the risk of obesity. Growth patterns through infancy and toddler period (1–2 years) are indicative of body fat, while growth patterns beyond infancy are less indicative of fat-free mass.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12887-023-04155-2.