The influence of maternal macronutrient balance and dietary glycemic index (GI) on neonatal body composition has received little study. We hypothesized that the overall quantity and quality of macronutrients, particularly carbohydrate, in the maternal diet could have trimester-specific effects on neonatal growth and body composition in women at risk of gestational diabetes. Maternal diet was assessed using 3-day food records in mid (n = 96) and late (n = 88) pregnancy as part of the GI Baby 3 study. Neonatal body composition was assessed by air-displacement plethysmography within 48 h of birth, adjusted for length, and expressed as fat mass index (FMI) and fat-free mass index (FFMI). In mid pregnancy, higher maternal intake of carbohydrate energy was negatively correlated with infant FFMI (p = 0.037). In late pregnancy, higher dietary GI was associated with lower FFMI (p = 0.010) and higher carbohydrate energy predicted lower FMI (p = 0.034). Higher fat intake (%E) and saturated fat, but not protein, also predicted neonatal body composition (higher FFMI in mid pregnancy and higher FMI in late pregnancy). Depending on pregnancy stage, a high carbohydrate-low fat diet, particularly from high glycemic sources, may reduce neonatal indices of both lean mass and adiposity. ; published_or_final_version