Allogeneic hematopoietic stem cell transplantation is used in treating certain malignant and non-malignant diseases. Chimerism after allogeneic haematopoietic stem cell transplantation is a condition, in which recipient and donor cells are present in recipient’s body. Chimerism analysis enables early detection of complications, such as disease relapse, graft-versus-host disease and graft rejection. Chimerism monitoring is therefore important for assessment and prediction of successfulness of hematopoietic stem cell transplantation and enables earlier intervention and thus the possibility of a patient being cured is higher. In our study we determined the usefulness of the AlleleSEQR (Celera, USA) kit and software AlleleSEQR Suite v1.1 Chimerism Analysis Software (Celera, USA) and KMRengine Chimerism Analysis Software (GenDx, Netherlands) for chimerism monitoring after hematopoietic stem cell transplantation with the use of quantitative PCR. Genomic DNA samples isolated from peripheral blood of 23 patients and their 23 donors were used for testing. Among 34 biallelic insertion/deletion polymorphisms informative markers were determined, which enables differentiation between donor and recipient genomic DNA. The proportion of recipient genomic DNA in several successive recipient samples, collected in different time intervals after transplantation, was then determined using the test for quantitative chimerism monitoring. The chimerism results were compared with patient’s clinical picture. The informativity of the assay was 100 % for all included donor/recipient pairs and was higher for unrelated pairs than for related. The results of the determination of proportion of genomic DNA matched with the patient’s clinical picture in 19 patients out of 23. The chimerism results did not always match with the clinical picture in four patients. In five patients we would need more successive samples to completely interpret the chimerism results. A smaller proportion of patients with mixed chimerism had graft-versus-host disease compared to the patients with complete chimerism. The sensitivity of the assay is high, as we detected 0,02 % chimerism, which enables earlier information about the change in proportion of recipient genomic DNA. The external quality control was successfully passed with the tested system. We can conclude that the test system is suitable for chimerism monitoring after allogeneic haematopoietic stem cell transplantation for Slovenian population of haematopoietic stem cell recipients.