**Abstract**

Allogeneic haematopoietic stem cell transplantation (allo-hSCT) is one of the most important therapeutic options for patients with both malignant and nonmalignant life-threatening rare disorders. Assessment of chimerism following allo-hSCT has been established as an indispensable tool for the clinical management of transplant recipients. The number of allo-hSCT among *CML* patients is decreasing due to tyrosine-kinase-inhibitor treatment. However, allo-hSCT in adult and paediatric patients with AML, ALL, and different non-malignant diseases is still increasing. For sex-independent patient chimerism monitoring, PCR-based short tandem repeat (PCR-STR) DNA markers with subsequent fragment analysis ('FA') and SYBR Green-based real-time PCR (SNPs or NPs markers of DNA) ('RQ PCR') were used. Specific features of chimerism assessment in non-malignant (n = 74) and malignant (n = 169) diseases were monitored by 'FA'. Complete and mixed chimerism was monitored also by SYBR Green-based realtime PCR method ('RQ PCR') (n = 188). By comparing the results of two chimerism monitoring methods ('FA' and 'RQ PCR') (n = 65), the higher sensitivity for the detection of the autologous DNA markers was observed by 'RQ PCR' (<1%) than 'FA' (1–5%). The lower detection limit of mixed chimerism could reveal an eventual relapse earlier. But the quantification of donor's DNA markers is more precise estimated by the FA.

**Keywords:** allo-hSCT, chimerism monitoring, diallelic indel polymorphisms, PCR-STR, rare diseases
