Abstract This study aimed to investigate the clinical characteristics and risk factors for graft rejection after keratoplasty in Asian patients. We enrolled 730 cases (566 patients) of penetrating keratoplasty (PK, N = 198), Descemet’s stripping automated endothelial keratoplasty (DSAEK, N = 277), non-Descemet’s stripping automated endothelial keratoplasty (nDSAEK, N = 138), and Descemet’s membrane endothelial keratoplasty (DMEK, N = 117). The incidence, clinical characteristics, and possible risk factors of graft rejection were analyzed. Overall, graft rejection occurred in 65 cases (56 patients, 8.9%). The incidence of rejection was highest with PK (3.45/100 person-years), followed by DSAEK (2.34), nDSAEK (1.55), and DMEK (0.24). Cox regression analysis showed that keratoplaty type, younger age, indications (such as failed keratoplasty and infection), and steroid eyedrop use were possible risk factors. Furthermore, PK had the highest hazard estimate of rejection, with significant differences between PK and the other groups (P = 0.018, DSAEK; P = 0.022, nDSAEK; and P < 0.001, DMEK). No significant difference was observed between DSAEK and nDSAEK groups (P = 0.829) in terms of graft rejecton. The DMEK group had the lowest hazard estimate of rejection, with significant differences between DMEK and the other groups (P < 0.001, PK; P = 0.006, DSAEK; and P = 0.010, nDSAEK), confirming the superiority of this procedure.