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To compare the outcomes of penetrating keratoplasty (PK) and lamellar keratoplasty (LK) in patients with mustard gas keratitis.A total of 78 eyes of 55 patients with mustard gas keratitis were included. Of these eyes, 27 (34.6%) underwent PK and 51 (63.4%) received LK. Keratolimbal allografts were performed in 11 and 30 eyes of the PK and LK groups, respectively. The study groups were compared in terms of best spectacle-corrected visual acuity, refractive error, and keratometry readings. The Kaplan–Meier survival curve and log-rank test were used to evaluate and compare the cumulative incidence of rejection-free graft survival and graft survival in PK and LK.At the time of keratoplasty, the mean patient ages were 40.3 ± 4.5 years and 43.4 ± 8.3 years in the PK and LK groups, respectively (P = 0.08). The patients were followed-up for 53.2 ± 27.5 and 40.4 ± 29.6 months, respectively (P = 0.09). At the last follow-up, the 2 study groups were comparable with respect to best spectacle-corrected visual acuity (P = 0.87), refraction (P = 0.08), and keratometric astigmatism (P = 0.27). At the 33-month follow-up examination, the rejection-free graft survival rates were 33.6% in the PK group and 90% in the LK group, with mean durations of 34.6 and 84.8 months, respectively (P < 0.001). Moreover, the graft survival rates were 77.3% and 91.7%, with mean durations of 67.5 and 76.1 months, respectively (P = 0.03). Three eyes that had received LK underwent PK because of significant interface haziness.LK is preferred to PK in the majority of mustard gas victims. However, PK should always be performed in certain conditions.