The effect of folinic acid (FA) on toxicity secondary to the use of methotrexate (MTX) for the prevention of graft-versus-host disease (GVHD) has not been determined. We retrospectively analyzed data from 111 patients who received allogeneic bone marrow transplantation (allo-BMT) in our institution. Fifty patients did not receive FA (non-FA), 37 received FA four times (low dose, LD-FA), and 24 received FA 25 times (high dose, HD-FA) in BMT. No significant differences were observed in the severity of stomatitis after allo-BMT among the three groups while the median of peak value of ALT in HD-FA was significantly lower (P = 0.031). The median time to neutrophil engraftment after allo-BMT in the HD-FA group was significantly shorter than that in the non-FA group (P = 0.034). No significant difference in the median time to neutrophil engraftment was observed between the LD-FA and non-FA groups (P = 0.44). Stepwise multiple regression analysis revealed that the determinants of the shorter duration of neutropenia were transfused total nucleated cell dose (P = 0.001) and the administration of HD-FA (P = 0.036). There was no significant difference in 3-year overall survival among the three groups. Frequent administration of FA may reduce the time to neutrophil engraftment after hematopoietic stem cell transplantation.