The incidence of long-term oral complications after hematopoietic SCT (HSCT) varies between 60 and 100%. The aim of this study was to compare the salivary secretion rate and the contribution of known risk factors for a low salivary secretion rate 1 year after HSCT in children conditioned with fractionated TBI (fTBI) and in children conditioned with single-dose TBI (sTBI). The study involved 44 patients, 27 conditioned with sTBI and 17 conditioned with fTBI. The unstimulated and stimulated salivary secretion rates (USSRs and SSSRs) were estimated before HSCT and at 1-year follow-up. Risk factors that may have influenced the salivary secretion rate were recorded. An SSSR of ≤0.5 mL/min and a USSR of ≤0.1 mL/min were chosen as cut-off points for salivary dysfunction. The median reduction in stimulated salivary flow 1 year after HSCT was 56% in the sTBI group and 12% in the fTBI group (P=0.003). The median reduction in unstimulated salivary flow 1 year after HSCT was 74% in the sTBI group and 33% in the fTBI group (P=0.003). In the multivariate model, a significant correlation between both sTBI (odds ratio (OR)=6.49, 95% confidence interval (CI)=1.40-30, P=0.014) and seropositivity of the recipient for 3-4 herpesviruses (OR=6.57, 95% CI=1.26-34, P=0.021) and a low stimulated salivary secretion rate (<0.5 mL/min) was found 1 year after HSCT.