To measure lamina cribrosa thickness (LCT), lamina cribrosa depth (LCD) and subfoveal choroidal thickness (SFCT) by imaging posterior ocular structures in pediatric cases with isolated unilateral iris coloboma and to investigate the differences as compared with healthy contralateral eyes of these cases (fellow eyes) and healthy control eyes. Methods: This cross-sectional, comparative prospective study included seven children (age range, 9-17 years) with unilateral isolated iris coloboma. The healthy contralateral eyes of these cases formed the fellow group. An age-matched (age range 8-17 years) control group (n=9), including children with both eyes having either normal or corrected-to-normal visual acuity, was formed. A detailed ophthalmic examination was performed. The posterior ocular segments were evaluated using spectral domain-optical coherence tomography (SD-OCT) with enhanced depth imaging (EDI) technique. Results: The SFCT was 372.0±48.8 µm, 375.3±44.0 µm, and 386.5±71.8 µm, respectively, and the LCD was 362.4±68.3 µm, 354.4±47.1 µm, and 350.7±38.1 µm, respectively, in the coloboma, fellow, and control eyes. There was no difference between the groups regarding SFCT and LCD. The mean LCT was significantly thinner in the coloboma eyes (200.2±9.5 µm) than in the fellow (238.8±26.7 µm; p=0.023) and control eyes (240.0±12.9 µm; p<0.001). The LCT showed no significant correlation with age, axial length or spherical equivalent. Conclusion: Better visual prognosis is expected in isolated iris coloboma. However, detailed examinations using new technologies, such as SD-OCT, may reveal some structural changes. Longitudinal studies are required to understand if a thinner LCT in coloboma eyes is associated with any future problems.