More than 145 European hematopoietic SCT programs have received JACIE (Joint Accreditation Committee for ISCT Europe and EBMT) accreditation since 2000, demonstrating compliance with FACT (Foundation for the Accreditation of Cell Therapy)-JACIE international standards. The association of JACIE with improved patient outcome was recently documented. However, conditions in which quality management systems were introduced and the actual benefits remain to be fully evaluated. Our study focuses on one aspect of quality management: introduction and use of indicators. Through a questionnaire sent to JACIE-accredited centers and responses from 32 programs (or 40%), we identified 293 indicators, including 224 (76%) that were introduced during the preparatory phase of JACIE accreditation. Indicators were associated with the following processes: measurement, analysis and improvement (54/293 or 18%); donor collection (49/293 or 16%); processing and storage of cell therapy products (37/293 or 12.5%); and administration of hematopoietic progenitor cells (67/293 or 23%). Mapping revealed an uneven distribution of indicators across the different subprocesses that contribute to this highly specialized medical procedure. Moreover, we found that only 101/293 indicators (34%) complied with the rules for implementation of a quality indicator, as defined by the FDX 50-171 standard. This suggests that risks to donors/recipients are unevenly monitored, leaving critical medical steps with low levels of monitoring.