The evaluation of minimal residual disease (MRD) is increasingly gaining ground in the prognostic assessment of childhood acute lymphoblastic leukemia (ALL). We studied MRD by metaphase-fluorescent in situ hybridization (FISH) in 41 children with ALL. At diagnosis, all patients were karyotyped by standard G-banding and studied with comparative genomic hybridization (CGH). Standard cytogenetic preparations were used for FISH. Eleven children were FISH-positive at some point post-induction. One of the eleven had a bone marrow (BM) relapse, and another a central nervous system (CNS)-relapse at the end of maintenance therapy, while the others remain in continuous complete remission (CCR). Five of the eleven FISH-positive were positive also after cessation of therapy, but none have relapsed. Of the 30 children with no FISH-detectable MRD post-induction, 2 have relapsed. We show that despite the presence of mitotically active blasts from the original leukemic clone during or after treatment, most of the children in our series remain in CCR although no action is taken to intensify or prolong the treatment.