Abstract Purpose of the work: To assess bone mineral density (BMD) in girls with menstruation disorders in the first years after menarche and to demonstrate that BMD value may be one of the indicators confirming an early diagnosis of hypothalamic hypogonadism or androgenisation complex. Material and methods: The research included 155 girls at the ages of 16-17, observed due to rare menstruation or secondary amenorrhea. In case of 71 girls functional, hypothalamic disorders were found (Group A), in 35 girls increasing androgenisation features were diagnosed additionally (Group B), and 49 healthy girls represented Group C – control group. BMI was determined, as well as FSH, LH, T, E2, PRL concentrations and the BMD test of lumbar spine section was made in all of the cases. Research results: The average values of BMI and BMD in Group A were the lowest compared to Group B (p<0.001) and Group C (p<0.001). E2 concentrations in Group A was the lowest and in Group B – the highest (p<0.001). T concentrations in Group B girls was the highest and SHBG – the lowest compared to Groups A and C (p<0.001; p<0.01). FSH concentrations in Group A were the lowest compared to Groups B and C (p<0.01), while LH in Group B was the highest (p<0.001; p<0.01). Basic PRL concentrations were not essentially different. In groups (A+B+C) together, a statistically significant correlation between BMD and BMI values was found (r=0.67; p<0.001), E2 (r=0.38; p<0.01) and T (r=0.56; p<0.001). Conclusions: Low bone mineral density value compared to the age value may signify long-term hypoestrogenism, and high value – a complex of metabolic disorders with high concentration of androgens. Therefore, bone mineral density may be a reliable and highly sensitive metabolic and hormonal indicator of menstruation disorders of hypothalamic, functional type or androgenisation complex.