This follow-up study confirms our previous findings that the ER-alpha PvuII polymorphism (Pp) modulates the association between exercise and bone mass. The differences in bone properties of girls with consistently low physical activity (LLPA) and consistently high physical activity (HHPA) were evident only in those bearing the heterozygote ER-alpha genotype (Pp). In particular, areal bone mineral density of the total femur, bone mineral content and areal bone mineral density of the femoral neck, and bone mineral content and cortical thickness of the tibia shaft were significantly (p < .05) lower in the Pp girls with LLPA than in their HHPA counterparts. These findings might partly explain the genetic basis of human variation associated with exercise training.