Purpose: To compare clinical outcomes of two methods of corneal transplantation, penetrating keratoplasty (PK) versus lamellar keratoplasty (LK), in patients with delayed-onset mustard gas keratitis (MGK).Methods: In this retrospective, comparative, interventional case series, 78 eyes of 55 victims of chemical warfare with delayed-onset mustard gas keratopathy who underwent PK or LK were enrolled. Two groups were compared in terms of best spectacle-corrected visual acuity (BSCVA), refractive error, and keratometric readings. The cumulative incidences of PK versus LK rejection-free graft survival, as well as graft survival were used to evaluate and compare the results.Results: At the time of keratoplasty, mean age was 40.3±4.5 years in the PK group and 43.8±4.3 years in the LK group (P=0.08), the patients were followed for 53.2±27.5 and 40.4±29.6 months, respectively (P=0.09). At the last follow-up, both groups were comparable in terms of to BSCVA (P=0.87), refraction (P=0.08), and keratometric readings (P=0.27). The rejection-free graft survival rate was 33.6% in the PK group and 90% in the LK group at 33 months with a mean length of 34.5 and 84.8 months, respectively (P<0.001). At the same follow-up examination, the graft survival rate was 77.3% and 91.7% with a mean length of 67.5 and 75.1 months, respectively (P=0.03). Three eyes that had received LK required PK because of significant interface haze formation.Conclusion: LK is preferred to PK in the majority of mustard gas victims. However, PK may inevitably be performed in some conditions.