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Objective To assess whether add-back therapy with norethindrone acetate (n. acetate) or n. acetate plus conjugated equine estrogens is superior to maintain bone health in adolescents and young women using gonadotropin-releasing hormone agonists (GnRHa) for endometriosis. GnRHa are associated with deleterious effects on bone. Hormonal add-back may mitigate these effects. Methods Adolescents and young women (n=51) received a random, double-blind assignment to add-back with n. acetate (5 mg/d) plus conjugated equine estrogens (0.625 mg/d) or n. acetate plus placebo for 12 months. Body composition, bone mineral content, and bone mineral density (BMD) were obtained by dual-energy X-ray absorptiometry (DXA) every 6 months. Quality-of-life measures were collected every 3 months. Intention-to-treat comparison of outcomes was conducted by repeated-measures ANOVA. Results Thirty-four adolescents and young women completed the trial; dropouts did not differ from. BMD was normal at baseline. At 12-months, total body bone mineral content and BMD had increased in the n. acetate plus conjugated equine estrogens group (bone mineral content +37g, p<0.001 and BMD +0.012 g/cm2, p=0.05), but not in those receiving n. acetate plus placebo (bone mineral content p=0.19 and BMD p=0.95). Lean mass increased only in those receiving conjugated equine estrogens (+1.4kg, p=0.001). Improvements in physical functioning domains of quality-of-life assessments were greater with n. acetate plus conjugated equine estrogens (p=0.005). No differences were seen at the hip or lumbar spine by DXA. No significant adverse events occurred. Conclusions Hormonal add-back successfully preserved bone health and improved quality of life for adolescents and young women with endometriosis during 12 months of GnRHa therapy. Combination n. acetate plus conjugated equine estrogens add-back appears to be more effective for increasing total body bone mineral content, areal BMD, and lean mass than n. acetate monotherapy. Clinical Trial Registration ClinicalTrials.gov;www.clinicaltrials.gov, NCT00474851.