A retrospective analysis of the relationship between the initial classification according to either FAB or WHO criteria, the presence of risk factors and the type of therapy including stem cell transplantation (SCT) on the survival was performed in a group of 106 patients with primary myelodysplastic syndrome (MDS) of FAB RA subtype. Allogeneic SCT early in the course of the disease did not significantly affect median survival in RA patients evaluated either according to FAB criteria (63.2 months in 17 SCT patients versus 64.4 months in 89 non-transplanted (non-SCT) patients) or in subgroups classified separately according to WHO (64.0 months in SCT versus 91.0 months in non-SCT RA patients and 66.2 months in SCT versus 43.0 months in non-SCT refractory cytopenia with multilineage dysplasia (RCMD) patients) or International Prognostic Scoring System (IPSS) criteria despite decreased incidence of leukemic transformation (5% in SCT versus 32% in non-SCT patients). Neither univariate or multivariate analysis of different clinical and laboratory parameters revealed a significant effect of SCT on 3 or 5 years survival in RA patients. The most probable explanation was a relatively high rate of transplantation related mortality (41%) on one hand together with a slow disease progression towards leukemia (24% at 5 years in non-SCT) on the other hand. A more refined stratification of patients based on the combined WHO morphology classification and IPSS cytogenetic criteria revealed subgroup of 11 non-SCT patients with RCMD and poor karyotype with median survival significantly different from that in five SCT patients (9.2 months in non-SCT versus 89.3 months in SCT, P=0.05). Thus, combined WHO morphology/IPSS cytogenetics criteria may be helpful for identification of the high risk patients with the RA group who may benefit from early SCT despite the relatively high incidence of SCT-related complications.