The International Obesity Taskforce (IOTF) recommends using age- and gender-specific body mass index (BMI) cut-points for defining the prevalence of overweight and obesity in children. These are given in both 6- and 12-month age intervals. Since the BMI-for-age curves are nonlinear, a degree of bias will be introduced when age intervals are wide. We aimed to quantify this bias in prevalence estimates in 2178 Australian children aged 4-12 years using 12- versus 6-month age intervals. Using the 12-month interval, the prevalence of overweight and obesity was underestimated by 1.4% compared to the 6-month interval estimates; however, this was age-dependent. It overestimated prevalence for 4-year olds, but underestimated it for older ages by up to 2.6%. Overweight prevalence was generally affected more than obesity prevalence. The use of different age intervals for IOTF cut-points introduces a small but systematic bias in prevalence estimates of overweight and obesity.