There are different drug combinations and conditioning regimens in lymphoma transplants. However, no randomized data is available to demonstrate the superiority of any regimen and the optimal choice is unknown. In this analysis, we compared the efficacy, toxicity and the survival outcomes of the BEAM and the high dose ICE (hdICE) conditioning regimens in relapsed NHL and relapsed/refractory Hodgkin Lymphoma patients undergoing auto-SCT. 83 patients with relapsed/refractory HL or relapsed NHL who were treated with Auto-SCT between 2006 and 2016, were analyzed retrospectively. 52 patients (62.7%) received BEAM, while 31 patients (37.3%) received hdICE. Between two groups there is no significant difference in age, gender, diagnosis, disease stage, chemosensitivity, ECOG performance status, time from diagnosis to transplant, salvage regimens and previous lines of chemotherapy. After a median of 59-month follow-up, PFS and OS rates of both groups were similar (5-year PFS was 51.6% in BEAM group, 48.8% in hdICE group,p = 0.71; 5-year OS was 58% in BEAM group, 54.8% in hdICE group,p = 0.93). The median neutrophil (11 vs. 10 days,p = 0.06) and platelet engraftment (13 vs. 11 days,p = 0.01) was faster and demand of transfusions were lesser in hdICE group (p = 0.03). However, severe renal toxicity was significantly higher in hdICE group in our study (p = 0.01). hdICE conditioning regimen may be used as an alternative to BEAM, with similar survival outcomes and toxicity profile, especially transplant centers that experience some difficulties in the availability of the carmustine.