Although current treatments can induce clinical complete remissions in the vast majority of patients with indolent lymphoma, most of them actually relapse, because of the persistence of residual tumor cells which are undetectable using conventional diagnostic procedures. Polymerase chain reaction (PCR)-based methods are increasingly used for minimal residual disease detection (MRD), and provide useful prognostic information. In this review, current approaches for MRD detection in indolent lymphomas are summarized. In addition, the prognostic aspects of molecular monitoring after transplantation procedures are discussed. The experience accumulated over the past decade shows that PCR analysis has a prognostic impact in several therapeutic programs including conventional and high-dose regimens. Major advantages coming from the introduction of molecular monitoring in clinical programs have been: (1) a rapid evaluation of the anti-tumor activity of innovative treatments; and (2) an early identification of patients with a high-risk of disease recurrence.