Hereby we present methodological aspects and prognostic significance of minimal residual disease (MRD) monitoring in infant acute leuke- mias. Based on our own experience we made algorithm for detection of MRD in this group of patients. We conclude that general concordance between MRD detection by flow cytometry and real-time polymerase chain reaction (PCR) for fusion gene transcripts achieved 87.0 %. Concordance was significantly lower during induction in comparison to consolidation/intensification and relapse treatment (78.6; 90.4 and 93.4 %, correspondingly; p = 0.002). It was not dependent on presence of normal B-cell precursors. Concordance between MRD results ob- tained by qualitative real-time PCR in bone marrow and peripheral blood samples was 84.5 %. Interestingly, all discrepant results (22 samples 15.5 %) were MRD-positive in bone marrow, but negative in peripheral blood. Despite high qualitative concordance rate between MRD detec- tion in bone marrow and peripheral blood samples we could not show prognostic value of MRD monitoring in peripheral blood by fusion gene transcripts. Multivariate analysis revealed that MRD-positivity at time-point 4 in bone marrow was the only significant and independent prog- nostic factor of unfavorable outcome in the observed group of patients (hazard ratio 7.326; 95 % confidence interval 2.378-22.565).