Background The extent of the obesity epidemic among youth is an important public health statistic which provides an indication of the future burden of non-communicable diseases. Many developing countries, including Albania, do not have systematic and repeated monitoring systems in operation. Methods The Balkan Survey of Inactivity in Children study is a population-based cross-sectional survey including Albanian children living in the four Balkan nation-states of Albania, Kosovo, FYR Macedonia and Montenegro. In total, 19,850 children from 49 schools were approached. The LMS method was used to provide body mass index (BMI), height, weight and waist circumference reference centiles for boys and girls. The World Health Organisation (WHO) and International Obesity Task Force (IOTF) age- and sex-specific BMI cut-points were applied to evaluate adiposity levels. Results A sample of 18,460 participants aged 6-16 years old was available for creation of the BMI for age and sex reference centiles. The prevalence of overweight (including obesity) in the full sample was 21% (95% CI: 20%-21%) according to IOTF cut-off points and 28% (95% CI: 28%-29%) at WHO cut-off points. Overweight/obesity levels where higher in boys than in girls irrespective of the cut-off points applied (p<0.001). Noticeable between-country differences were observed with a prevalence of overweight/obesity of 40% (95% CI: 38%-42%) in Montenegro but only 20% (95% CI: 19%-21%) in Kosovo (WHO cut-off points). Conclusions Overweight/obesity is highly prevalent in Albanian children and adolescents. The apparent sex and country differences may inform public health actions.