Background Endothelial cell density and morphology vary across ethnic groups. Aim This article investigates the corneal endothelial cell density and morphology in healthy Libyan eyes. Methods A 3-month cross-sectional observational study was conducted at Benghazi Teaching Eye Hospital, involving 198 eyes of 100 healthy Libyan participants. The noncontact Topcon specular microscope (SP-1P model) was used to assess the following parameters: the mean central corneal thickness (CCT), the mean cell density (MCD), the mean coefficient of variation (CV%), and the mean percentage of the hexagonal cell (Hex [%]). The variables were analyzed in relation to age and gender using the Statistical Package for the Social Sciences (SPSS version 25.0) Results The mean age of participants in this study was 47.4 ± 13.8 years (range 21–75 years). The mean CCT was 516.45 ± 43.04 μm, the MCD was 2664.30 ± 371.26 cells/mm2, the mean CV% was 32.3% ± 3.7, and the mean Hex (%) was 52.8% ± 9.6. There was no statistical difference in the age, CCT, and MCD across genders. Whereas CV (%) and Hex (%) showed significant gender differences (p < 0.01 for both). There was a significant negative weak correlation between CCT (r = –0.10) and age, as well as a significant negative moderate correlation between MCD and Hex (%) with age (r = –0.36 and r = –0.31, respectively). CV% exhibited a significant, moderately positive association with age (r = 0.35). The higher endothelial cell loss rate of 8.4% was in the third decade of life whereas other age groups ranged between 1.1 and 2.7%. Conclusion The normative data for the endothelium of Libyan eyes are reported, which can be used as a baseline for future studies.