Background Achievement of target blood concentrations of cyclosporine (CsA) early after transplantation is known to be highly effective for reducing the incidence of acute graft versus host disease (aGVHD). However, no research has been conducted for predicting elapsed time from low CsA concentration to aGVHD occurrence. The objective of this study was to investigate the risk of aGVHD according to elapsed time from low CsA concentrations in children with allogenic hematopoietic stem cell transplantation (HSCT). Methods The outcomes of 61 consecutive children who underwent allogeneic HSCT and received CsA as prophylaxis against aGVHD between May 2012 and March 2015 were retrospectively evaluated; the main outcome was any association between elapsed time from low CsA concentrations to aGVHD occurrence. Elapsed time was defined as follows: one week (0–6 days), two weeks (7–13 days), or three weeks (14–20 days), and the incidence of aGVHD was examined for the first three months after transplantation. ResultsIn children whose mean CsA concentration after the allogenic HSCT did not reach the initial target concentration, the adjusted odds ratio for developing aGVHD within one week was 12.3 (95% confidence interval [CI]: 2.7–56.0). The AORs for developing aGVHD between 7 and 13 days and between 14–20 days were 90.8 (95% CI: 8.3–999.9) and 28.1 (95% CI: 2.4–333.1), respectively. Conclusions Careful attention needs to be paid to the elapsed time after low CsA concentrations are detected to prevent aGVHD.