Busulfan, cyclophosphamide and etoposide (BuCyE) is a commonly used conditioning regimen for autologous stem-cell transplantation (ASCT). This multicenter, phase 2 study examined the safety and efficacy of BuCyE with individually-adjusted busulfan based on pre-conditioning pharmacokinetics. The study initially enrolled Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL) patients 18–80 years, but was amended due to high early treatment-related mortality (TRM) in patients >65 years. BuCyE outcomes were compared with contemporaneous recipients of carmustine, etoposide, cytarabine and melphalan (BEAM) from the Center for International Blood and Marrow Transplant Research. Two hundred seven subjects with HL (n=66) or NHL (n=141) were enrolled from 32 centers in North America, and 203 underwent ASCT. Day 100 TRM for all subjects (n=203), patients >65 years (n=17), and patients ≤65 years (n=186) were 4.5%, 23.5% and 2.7%, respectively. The estimated 2-year PFS was 33% for HL, and 58%, 77% and 43% for diffuse large B-cell lymphoma (DLBCL; n=63), mantle cell lymphoma (MCL; n=29) and follicular lymphoma (FL; n=23), respectively. The estimated 2-year OS was 76% for HL, and 65%, 89% and 89% for DLBCL, MCL and FL, respectively. In the matched analysis, two-year TRM was 3.3% for BuCyE and 3.9% for BEAM, and there were no differences in outcomes for NHL. Patients with HL had lower 2-year PFS with BuCyE, 33% (95% CI: 21–46%) than BEAM, 59% (95% CI: 52–66%), with no difference in TRM or OS. BuCyE provided adequate disease control and safety in B-cell NHL patients ≤ 65 years, but produced worse PFS in HL patients when compared with BEAM.