Menstrual dysfunction (MD) in female athletes might be indicative of the syndrome of relative energy deficiency in sports (REDs), associated with, e.g., impaired bone health, an increased risk of injury, and decreased performance. In the present study, we investigated differences in objective indicators of REDs, bone mineral density (BMD), and blood-based biomarkers in female elite athletes with self-reported MD or eumenorrhoea (CON) from mixed sport disciplines. Athletes reporting < 9 menstrual bleedings within the last year were recruited in the MD group, whereas eumenorrheic athletes with no symptoms of eating disorders were recruited for CON. Of the 24 athletes included, 19 completed the examinations (9 MD; 10 CON, mean age +/- SD: 24.8 +/- 5.5 years). Dual-energy x-ray absorptiometry (DXA) was used to assess body composition and BMD. Fasted rested blood sampling was performed to assess blood-based biomarkers of bone and endocrine status. Two MD athletes were excluded from the analysis due to suspected polycystic ovary syndrome. Results showed that MD was associated with lower BMD Z-scores across several sites compared to CON (between-group differences +/- SE); whole-body Z-score: -1.4 +/- 0.5, p = 0.03; lumbar spine Z-score: -1.4 +/- 0.6, p = 0.03; proximal femur: -1.6 +/- 0.6, p = 0.02). However, no between-group differences in biomarkers of bone turnover were observed. MD was associated with lower plasma concentrations of luteinizing hormone (p = 0.02), prolactin (p < 0.001), and free T-3 (p = 0.01). In conclusion, the present data indicate impairment in bone health and endocrine homeostasis in female elite athletes with current MD and underline the importance of MD as a potential indicator of REDs in female elite athletes. Furthermore, these findings call for regular screening of symptoms for early identification of athletes at risk in all sport disciplines and more education of athletes, coaches, and medical staff regarding this issue.