PurposeThe following is a comparative analysis on the treatment outcomes of corneal perforations using amniotic membrane transplantation (AMT) or penetrating keratoplasty (PK).MethodsThis monocentric retrospective study was performed at the Department of Ophthalmology, University Hospital Ulm, Germany. A total of 78 eyes of 78 patients were included. Thirty-nine eyes received an AMT, and 39 patients were treated with a PK. Primary outcome was recurrence of perforation. Secondary outcomes were patient mortality and visual acuity.ResultsNo statistically significant difference was observed with regard to a recurrence of perforation between the two groups (26% in AMT vs 23% in PK,p> 0.99). The time of recurrences was within the first two years and did not differ statistically (p= 0.97). In addition, a proportional hazards model with cox regression regarding recurrent perforation showed no significant differences (p= 0.5). After AMT, 41% and after KP, 28% of the patients died during follow-up (p= 0.2), respectively. The Charlson Comorbidity Index (p< 0.0001) and the age at the time of surgery (p= 0.0002) were statistically significantly higher in those who were deceased. A mean follow-up of 485 ± 517 days was recorded.ConclusionBoth surgical methods show good results and no statistically significant difference regarding recurrent perforation rate. About a third of the patients died during the follow-up period. The decision regarding the appropriate method should therefore be based on a combination of all factors.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00417-022-05914-0.