Fanconi anemia (FA) is an inherited DNA repair disorder associated with short stature and bone marrow failure, usually requiring hematopoietic cell transplantation (HCT). Although low bone mineral density (BMD) has been reported in leukemia patients after HCT, little is known about BMD in FA children after HCT (FA HCT). This study's goals were to compare BMD in FA HCT to BMD in healthy controls and in children who received HCT for hematologic malignancy (cancer HCT), and to test for associations between BMD and risk factors for bone loss. This cross-sectional study included 20 FA HCT, 13 cancer HCT, and 90 healthy controls, age-matched and <18 years old at evaluation. BMD Z-scores for total body (TBMD) and lumbar spine (LBMD) were measured by dual energy x-ray absorptiometry and adjusted for height-for-age Z-score (HAZ). FA HCT had lower mean TBMDHAZ Z-score (by .8 SD) and higher fraction with Z-score ≤ -1 than healthy controls (42% versus 11%). No LBMD deficits were detected. FA HCT and cancer HCT groups did not differ significantly in TBMD or LBMD Z-scores. In FA HCT patients, lower body mass index and lower percent fat were associated with lower BMD. This study highlights the importance of monitoring BMD to optimize bone health in FA patients.