A large proportion of the variation in bone mass can be explained by genetic factors. We analyzed the G to T substitution in the Sp1 binding site in the first intron of the collagen type Ialpha1 (COLIA1) gene in relation to bone mass. The genotypes GG, GT, and TT were determined in 148 Caucasian children and young adults. We performed dual energy X-ray absorptiometry twice (mean follow-up time 4.4 years), and speed of sound (SOS) was assessed by tibial ultrasonometry at follow-up. Genotype distribution was 104 (70%) GG, 40 (27%) GT and 4 (3%) TT. Carriers of the T-allele had a 0.5 SDS (standard deviation score) decreased bone mineral content (BMC) of total body (P = 0.001), and a 0.4 SDS decreased bone mineral density (BMD) for both lumbar spine (P = 0.04) and total body (P = 0.05). The genotype effect on BMD and BMC decreased after adjustment for height or body mass index. When we calculated apparent BMD, these differences diminished to 0.1 SDS and were no longer significant. T-allele carriers had shorter stature (0.4 SDS; P = 0.04) and smaller bones (0.5 SDS lower width of the lumbar vertebral body; P = 0.01). The T-allele was also associated with lower SOS (P = 0.03), independent of BMD and BMC, and lower lean body mass. Similar associations were found at follow-up. The change in BMD and BMC SDS between the first and second measurement did not differ between the GG and GT&TT group. In conclusion, the COLIA1 polymorphism in children and young adults is associated with several bone characteristics. However, at least a part of the COLIA1 effect on bone mass may be related to differences in frame size.