Hypotheses: Values of serum markers related to bone quality are abnormal in young female ballet dancers. Methods: In 13 elite Japanese female ballet dancers (average age, 22 years), markers related to bone quality were investigated. These included: serum homocystein (HC), a marker of increased oxidative stress; pentosidine (Pent), a marker of glycation-or oxidation-induced non-enzymatic cross-links; markers of bone metabolism (bone alkaline phosphatase, BAP; tartrate-resistant acid phosphatase 5b, TRAP5b) and bone mineral density (BMD). It was determined whether there is a relationship between bone quality markers' levels are related to amenorrhea and/or fatigue fractures. Results: Two dancers had fatigue fractures and 3 had a history of secondary amenorrhea. The average BMD was 1.305 ± 0.12 (g/cm 2 ), in all these cases the Z-score was higher than −1.0. Although the serum levels of BAP, TRAP5b, and HC were normal in all examined dancers, in 2 out of 3 dancers with a history of secondary amenorrhea, pentosidine serum levels were increased. No relationship between bone quality markers' levels and fatigue fractures was found. Conclusion: Latent deterioration of bone quality may occur in female athletes with secondary amenorrhea and otherwise normal BMD and calcium metabolism markers.