Long-term effects of type 2 diabetes mellitus (T2D) on bone health remain unclear. The objective of this study was to assess the possible association of bone mineral density (BMD) at multiple sites with T2D after correcting for several potential confounders such as age, sex, Tanner stage, and BMI known to affect BMD in adolescents with newly developed T2D. In this cross-sectional study, 17 children and adolescents with T2D and 59 age, sex, and BMI-matched controls were included. All subjects underwent dual-energy X-ray absorptiometry to measure regional and whole-body composition with Lunar Prodigy at the time of initial diagnosis. A BMD Z-score was calculated using data from healthy Korean children and adolescents after adjusting for height-for-age. The mean age of all subjects was 12.9+/-2.4 years (range, 8.3-18.3 years). BMDht Z-scores for lumbar spine and total body after adjusted for age, sex, BMI SDS, and Tanner stage were not significantly different between patients and controls. However, BMDht Z-scores for femur neck and bone mineral apparent density (BMAD) Z-scores of lumbar spine were significantly lower in T2D patients than those in healthy controls. HOMA-IR or HbA1c was not associated with BMDht Z-scores at multiple sites. BMDht Z-scores at multiple sites except femur neck in adolescents with newly developed T2D were similar to those in obese controls after adjustment for potential confounders.