Introduction We aimed to evaluate the bone mineral density (BMD) z scores of adolescents with atypical anorexia nervosa (AAN) and investigate the potential predictors of low BMD risk. Materials and methods Potential factors that might have an effect on the femoral neck and lumbar spine dual energy X-ray absorptiometry data of adolescents (11-18 years) with AAN were retrospectively evaluated. Results Among adolescents with AAN, 13 (34.2%) had a z score lower than - 1 and 25 (65.8%) had a z score equal or greater than - 1. When adolescents with a BMD score lower and higher than - 1 were compared, normal BMD group had a significantly higher mean lifetime maximum BMI (p = 0.0035). Similarly previous overweight history was significantly higher in the normal BMD group (p = 0.005). A positive correlation was found between femoral neck (p = 0.002, r: 0.546) and lumbar spine (p: 0.002, r: 0.505) z scores and lifetime maximum BMI. There was also a positive correlation between lumbar spine BMD scores and BMI at admission (p = 0.001, r: 0.540). Lumbar spine z scores and amenorrhea duration were negatively correlated (p: 0.002, r: - 10.867). Conclusion In the adolescent period similar to AN, AAN cases are also at risk for disordered bone health. In adolescents with AAN, BMI prior to the illness was estimated to be the significant parameter for the risk of low BMD. Special attention should be paid to the bone health of adolescents with AAN, especially for those who do not have a previous overweight history.