This study aimed to standardize a simple molecular method for evaluating the response to treatment in multiple myeloma (MM) patients after high dose chemotherapy. Fifty three patients enrolled in the GEM2000 protocol were studied for minimal residual disease (MRD) using both fluorescent-polymerase chain reaction (F-PCR) and flow cytometry. Most patients had achieved complete remission or very good response after autologous stem cell transplantation. The molecular analysis of immunoglobulin gene rearrangements at diagnosis and during the follow-up was carried out by F-PCR according to the Biomed-2 protocols. F-PCR could be used in 91% of the patients and the results were similar to flow cytometry. F-PCR was able to identify a group of patients with a better prognosis [progression-free survival (PFS) 67.86% in patients with negative F-PCR vs. 28%; P = 0.001], even amongst patients who achieved a complete response with negative immunofixation (PFS 75% vs. 25%; P = 0.002). Multivariate analysis identified the F-PCR result as the only variable to show a prognostic value when PFS was analysed. F-PCR of DHJ and light chain rearrangements of immunoglobulin genes is a feasible method for evaluating MRD in MM patients after intensive therapy. Achieving molecular response by F-PCR shows prognostic value.