The aim of this study was to determine the potential role of leukocyte telomere length as a biomarker for development of childhood obesity in a low‐income Latino population. A birth cohort of Latino children (N = 201) in San Francisco (recruited May 2006–May 2007) was followed until age 9 and assessed annually for obesity and dietary intake. Leukocyte telomere length was measured at 4 and 5 years (n = 102) and assessed as a predictor for obesity at age 9, adjusting for known risk factors. Furthermore, leukocyte telomere length at age 4 and 5 was evaluated as a possible mediator of the relationship between excessive sugar‐sweetened beverage consumption and obesity at age 9. Shorter leukocyte telomere length in preschoolers was associated with obesity at age 9 (adjusted odds ratio 0.35, 95% confidence interval 0.13–0.94) after adjustment for known risk factors. Telomere length mediated 11% of the relationship between excessive sugar‐sweetened beverage consumption and obesity. Shorter leukocyte telomere length may be an indicator of future obesity risk in high‐risk populations as it is particularly sensitive to damage from oxidative stress exposure, including those from sugar‐sweetened beverages.