Follistatin is a member of the activin-follistatin-inhibin hormonal system and is proposed to affect bone metabolism. However, data regarding the effect of follistatin on bone are relatively scarce and contradictory in humans. The purpose of the current study was to investigate possible associations of serum follistatin concentration with bone mineral characteristics in lean and physically active adolescent girls. Bone mineral density, body composition, resting energy expenditure and different energy homeostasis hormones in serum including follistatin, leptin and insulin were investigated. Significant relationships ( < 0.05) between serum follistatin (1275.1 ± 263.1 pg/mL) and whole-body (WB) bone mineral content (r = 0.33), WB areal bone mineral density (aBMD) (r = 0.23) and lumbar spine (LS) aBMD (r = 0.29) values were observed. Serum follistatin remained associated with LS aBMD independent of body fat and lean masses (r = 0.21; < 0.05). However, the follistatin concentration explained only 3% (R × 100; = 0.049) of the total variance in LS aBMD values. In conclusion, serum follistatin concentrations were associated with bone mineral values in lean adolescent girls with increased physical activity. Follistatin was an independent predictor of lumbar spine areal bone mineral density, which predominantly consists of trabecular bone.