High-dose therapy with autologous stem cell transplant (autoSCT) is standard therapy for relapsed/refractory Hodgkin lymphoma, although the optimal conditioning regimen remains uncertain. We conducted a retrospective analysis of 100 consecutive patients with relapsed/refractory Hodgkin lymphoma who underwent autoSCT between 1998 and 2009. There were 60 patients who received busulfan, melphalan and thiotepa (BuMelTt) conditioning and 40 who received other common regimens. There were no significant differences in patient characteristics between the two groups. With a median follow-up of 4.3 years, the 5-year overall survival (OS) was superior for patients who received BuMelTt versus other conditioning (73% vs. 44%, p = 0.05). BuMelTt was also associated with an improved 5-year progression-free survival (66% vs. 37%, p = 0.03). There were no differences in length of hospitalization, febrile neutropenia, hepatic veno-occlusive disease or 100-day non-relapse mortality (NRM). There were more cases of severe mucositis but fewer episodes of bacteremia with BuMelTt. Our results suggest that BuMelTt may be a superior conditioning regimen for autoSCT in Hodgkin lymphoma.