Many patients with follicular lymphoma (FL) achieve response after treatment but complete remission (CR) rates are very low. Thus the majority of them will relapse, mainly those in advanced stage disease, due to the persistence of residual disease. Therefore, this study had the following aims: to determine the presence of bcl-2/IgH rearrangement in peripheral blood of early and advanced stage FL patients after treatment and to correlate it with their clinical situation at the same moment. We obtained 100 consecutive peripheral blood samples from 30 FL cases and conducted molecular studies using two separate semi-nested PCRs for MBR and mcr rearrangements. These semi-nested PCRs for bcl-2/IgH rearrangement were able to detect one positive cell among 10,000 normal cells. Clinical and molecular evolution of patients diagnosed as early stage disease suggested that molecular response could be obtained even with conventional chemotherapy or radiotherapy. In this group of patients, 64% achieved molecular response in some point during follow-up. However, only 23% of patients diagnosed as advanced stage disease reached molecular response when treated with chemotherapy (with or without radiotherapy). Due to the low number of subjects assessed in this study, we only found a tendency to significance when clinical stage at the diagnosis was associated to molecular response (P = 0.095). We observed 100% of concordance between clinical remission and molecular response in patients after bone marrow transplantation or in those cases treated with monoclonal antibody anti-CD20. This retrospective study, performed in a restricted number of patients, suggests that molecular response can be obtained in FL patients diagnosed at early stage disease, even with conventional chemotherapy and radiotherapy. In advanced stage disease, concordance between clinical remission and molecular response was observed in the majority of patients after bone marrow transplantation or in those cases treated with monoclonal antibody anti-CD20. The prognostic significance of this data should be confirmed with extended follow-up and in a larger number of patients.