Recent innovations in treatment of multiple myeloma include autologous stem cell transplantation (ASCT) along with high dose chemotherapy (HDC). We undertook this study to estimate incremental cost per quality adjusted life year gained (QALY) with use of ASCT along with HDC as compared to conventional chemotherapy (CC) alone in treatment of multiple myeloma. A combination of decision tree and markov model was used to undertake the analysis. Incremental costs and effects of ASCT were compared against the baseline scenario of CC (based on Melphalan and Prednisolone regimen) in the patients of multiple myeloma. A lifetime study horizon was used and future costs and consequences were discounted at 5%. Consequences were valued in terms of QALYs. Incremental cost per QALY gained using ASCT as against CC for treatment of multiple myeloma was estimated using both a health system and societal perspective. The cost of providing ASCT (with HDC) for multiple myeloma patients was INR 500,631, while the cost of CC alone was INR 159,775. In the long run, cost per patient per year for ASCT and CC arms was estimated to be INR 119,740 and INR 111,565 respectively. The number of QALYs lived per patient in case of ASCT and HDC alone were found to be 4.1 and 3.5 years respectively.From a societal perspective, ASCT was found to incur an incremental cost of INR 334,433 per QALY gained. If the ASCT is initiated early to patients, the incremental cost for ASCT was found to be INR 180,434 per QALY gained. With current mix of patients, stem cell treatment for multiple myeloma is not cost effective at a threshold of GDP per capita. It becomes marginally cost-effective at 3-times the GDP per capita threshold. However, accounting for the model uncertainties, the probability of ASCT to be cost effective is 59%. Cost effectiveness of ASCT can be improved with early detection and initiation of treatment.