Allogeneic hematopoietic stem cell transplantation (alloHSCT) is a curative approach for multiple hematologic diseases. The success of alloHSCT is evaluated by analyzing the proportion of living donor cells in blood and bone marrow samples of the recipient (chimerism analysis). To monitor the engrafted cells, donor's individual genetic markers are analyzed in peripheral blood and bone marrow samples, usually by using short tandem repeat (STR) analysis. An alternative method to measure chimerism is based on insertion and deletion markers (InDels) analyzed by digital droplet PCR (ddPCR); however, this approach is rarely evaluated in clinical practice. In this study, we examined the usefulness of ddPCR-based chimerism analysis against the standard STR analysis in samples around day+30 after alloHSCT in clinical practice using peripheral blood and bone marrow samples. The median absolute difference between ddPCR and STR analysis was 0.55% points for bone marrow chimerisms and 0.25% points for peripheral blood chimerisms, respectively, including variation in the range of maximum 2% for both methods. The results of every single sample gave the same clinical message. According to our data, chimerism analysis by ddPCR has an excellent correlation with STR-based analyses. Due to its fast and easy applicability, the ddPCR technique is suitable for chimerism monitoring in clinical practice. © 2019 John Wiley & Sons Ltd.