The aim of the present study was to examine the associations of sugary drink consumption and its substitution with alternative beverages with body weight gain among young children predisposed to future weight gain. Secondary analysis of the Healthy Start Study, a 1·5-year randomised controlled trial designed to prevent overweight among Danish children aged 2−6 years (n 366), was carried out. Multivariate linear regression models were used to investigate the associations of beverage consumption with change in body weight (Δweight) or BMI(ΔBMI) z-score. Substitution models were used to extrapolate the influence of replacing sugary drinks with alternative beverages (water, milk and diet drinks) on Δweight or ΔBMI z-score. Sugary drink intake at baseline and substitution of sugary drinks with milk were associated with both Δweight and ΔBMI z-score. Every 100 g/d increase in sugary drink intake was associated with 0·10 kg and 0·06 unit increases in body weight (P=0·048) and BMI z-score (P=0·04), respectively. Substitution of 100 g/d sugary drinks with 100 g/d milk was inversely associated with Δweight (β=−0·16 kg; P=0·045) and ΔBMI z-score (β=−0·07 units; P=0·04). The results of this study suggest that sugary drink consumption was associated with body weight gain among young children with high predisposition for future overweight. In line with the current recommendations, sugary drinks, whether high in added or natural sugar, should be discouraged to help prevent childhood obesity. Milk may be a good alternative to sugary drinks with regard to weight management among young obesity-predisposed children.