Children with chronic diseases are at risk for low bone mineral density (BMD). There are no studies of BMD in children with congenital heart disease and particularly single ventricle (SV). Children with this defect are often treated with warfarin, suspected to negatively impact BMD in adults. We assessed BMD in patients with SV physiology and compared the BMD of subjects taking warfarin to those who were not. Subjects 5–12 years with SV were included. BMD z scores by dual-energy X-ray absorptiometry of the spine and total body less head (TBLH) were obtained. Calcium intake, activity level, height, and Tanner stage were assessed. Linear regression models and t tests were used to investigate differences between participants and normative data as well as between subjects’ subgroups. Twenty-six subjects were included and 16 took warfarin. Mean BMD z score at the spine was significantly lower than expected at −1.0 ± 0.2 (p < 0.0001), as was the BMD z score for TBLH at −0.8 ± 0.2 (p < 0.0001). Those results remained significant after adjusting for height. Subjects who were on warfarin tended to have lower BMD at both the spine and TBLH than those who were not, with a z score difference of 0.6 ± 0.46 at the spine (p = 0.106) and a difference of 0.4 ± 0.34 at TBLH (p = 0.132). BMD is significantly reduced in children with SV. Warfarin appears to lower BMD but the effect is less conclusive. Continued evaluation is recommended for these patients at risk for reduced bone density. Evaluation of other cardiac patients on warfarin therapy should also be considered.