Randomized multicenter trials in the area of hematopoietic stem cell transplantation (HSCT) face considerable challenges, therefore, their amount is relatively small. Most clinical guidelines are based on the data of multicenter registry studies or well-controlled prospective single-center non-randomized studies. To determine the criteria of a well-controlled single-center trial the results of which can be confirmed by a multicenter analysis, the total of 44 groups of patients from 22 cooperative studies in collaboration with EBMT were analyzed. The results of these studies were compared with single-center data and the results of the planned studies of RM Gorbacheva Scientific Research Institute of Pediatric Oncology, Hematology and Transplantation. In 43 % of cases significant differences were observed, whereby result-difference probability did not decrease with a rising number of patients in the single-center groups, but became higher (odds ratio 1.037; 95% confidence interval 1.001–1.074; p = 0.046), which highlights the differences in methods of single- and multicenter trials. While analyzing the reasons of significant results the following necessary criteria for high-quality single-center trials in the area of HSCT were formulated: 1) conditioning regimens and graft-versus-host disease prophylaxis (if they are not subject of the study) need to be consistent with the most frequently used practices; 2) groups of patients should be status-homogeneous; 3) the trial must not include the patients treated more than 5 years before the analysis; 4) patients should receive current antitumor therapy at pre- and post-transplantation stages; 5) each compared group should include more than 30–40 patients.