Background Bacillus Calmette-Guérin vaccine (BCG) induces a complex, pro-inflammatory immune response. Obesity is associated with low-grade inflammation. Aims The purpose of the study was to test whether BCG at birth has effects on infant growth and body composition. Study design, subjects, and outcome measures The Danish Calmette Study is a randomized, clinical trial. The study was conducted at three university hospitals and randomized 4262 children of gestational age ≥ 32 weeks to receive BCG within seven days of birth or to a no-intervention control group. Follow-up consisted of clinical examinations. Outcome measures were weight and length at 3 months, and weight, length, mid upper-arm circumference, and triceps and subscapular skinfold at 13 months. Data collectors were blinded to allocation. Anthropometric measurements were converted to z-scores using WHO reference population. Results Follow-up was 94% complete at 3 and 13 months after birth. The children were bigger than the WHO reference population. There was no effect of BCG on weight z-score at 13 months (− 0.028 [95% confidence interval: − 0.085 to 0.029], p = 0.34). There was no effect on weight and length at 3 months, or length, mid-upper-arm circumference, or triceps and subscapular skinfold at 13 months. Conclusion In this study, vaccination with BCG at birth did not have effects on child growth or body composition at 13 months. Trial registration www.clinicaltrials.gov, registration number NCT01694108.