Aim: To compare the outcomes of IntraLase-enabled top hat penetrating keratoplasty (IEK) versus retrospective results of manual top hat penetrating keratoplasty (TH-PKP) and conventional PKP. Patients/methods: This non-randomised prospective study included 94 eyes: 23 eyes underwent IEK, 36 TH- PKP and 35 conventional PKP. Preoperative and postoperative manifest refraction, uncorrected and best-spectacle corrected visual acuity (BSCVA), high-order ocular aberrations (HOA), endothelial cell counts and complications were analysed. Results: At 12 months of follow-up, the mean log MAR BSCVA was 0.32 (SD 0.31) in the IEK group, 0.53 (0.36) in the TH PKP group (p = 0.03) and 0.39 (0.30) in the conventional PKP group (p = 0.4). The mean spherical equivalent was similar between the groups and was less than -2.2 dioptres. The mean cylinder was similar in the IEK and conventional PKP group (3.6 (1.9) dioptres and 4.1 (1.8) dioptres, respectively), and was significantly lower than the TH-PKP group (5.1 (3.2) dioptres, p = 0.04). The complications rate and high-order ocular aberrations were similar between the three groups studied. The mean endothelial cell loss was significantly lower at 12 months of follow-up in the IEK and the TH- PKP groups versus conventional PKP (32.4% and 22.3% vs 40.8%, respectively) (p = 0.05). The mean time to suture removal was 4.1 (1.2) months in the IEK group and 3.9 (1.5) months in the TH-PKP group versus 9.7 (1.1) months in the conventional PKP group (p<0.0001). Conclusions: IEK is a safe and stable procedure. It results in higher endothelial counts and faster suture removal in comparison with the conventional PKP, and has less astigmatism and better BSCVA in comparison with the manual TH-PKP.