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The aim of this study was to analyse the chimaerism kinetics in children after allogeneic HSCT performed in Vilnius University Children's Hospital. The review focused on the relationship of chimaerism kinetics and clinical course. In addition, the impact of different pre-transplant variables on the chimeric state was proven. Patients and methods. The patients' cohort consisted of 19 children with malignant and non-malignant haematological disorders. Stem cells were procured from HLA-identical siblings and HLA-matched unrelated donors. Chimeric state was assessed by means of multiplex-PCR using STR polymorphisms. The analysed DNA was extracted from whole blood leukocytes. Results. Complete DC developed in 47.4% (9/19), MC did in 52.6% (10/19) of patients. The children with non-malignant disorders showed stable and increasing MC patterns meanwhile the leukaemic patients revealed exclusively increasing MC. Development of MC was consistent with non-malignant disorder (p = 0.033) and non-myeloablative conditioning (p = 0.033). In 2 of 5 non-malignant patients MC was followed by graft rejection whereas in patients with haematological malignancies MC was found to be strongly associated with leukaemic relapse (p = 0.002). Both events were the principal factors that limited OS in patients with MC to 50.0%. On the contrary, patients with DC succumbed mostly to the transplant related mortality (p = 0.049) resulting in similar OS of 55.6%. Conclusions. Chimeric state had no significant impact either on the EFS (p = 0.435) or on the OS (p = 0.601). The results confirmed the reports of other European centres that studied chimaerism kinetics and are consistent with the current transplant practice in Europe. [ABSTRACT FROM AUTHOR]