Background: The negative impact of anorexia nervosa (AN) on bone health is well defined. However, there are very few studies evaluating the effect of constitutional thinness on bone health, especially in the adolescent period and in the male gender. The aim of this study is to compare the bone mineral density (BMD) measurements of adolescents with AN and with constitutional thinness. Methods: Between April 2013 and March 2014, 40 adolescents with AN and 36 adolescents with constitutional thinness participated in the study. The femoral neck and lumbar spine BMD were measured by dual energy X-ray absorptiometry (DXA). Results: Mean lumbar z and BMD scores of adolescents with constitutional thinness were significantly lower than in adolescents with AN, whereas the mean femoral z and BMD scores were not significantly different. When males were compared separately, lumbar z and BMD values of the constitutionally thin group were found to be significantly lower than in the AN group. This difference was not significant for females. Conclusions: The difference between the male and female results of our study suggested two hypotheses. The significantly lower BMD values in constitutionally thin boys are attributed to their longer duration of low body mass index (BMI). Although the duration of low BMI is also longer for constitutionally thin girls, similar BMD values of AN and constitutionally thin female groups are attributed to the additional negative impact of estrogen deficiency on the bone health of girls with AN.