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To compare central corneal thickness between eyes with congenital glaucoma and normal controls and to correlate this parameter with corneal diameter and axial length.Eyes of consecutive children with congenital glaucoma with previous glaucoma surgery and eyes of children with inadequacy of lacrimal drainage system with age less than 3 years old were examined under inhalatory general anesthesia. Complete ophthalmologic examination, central corneal thickness, axial length, and corneal diameter measurements were performed. All patients presented with intraocular pressure (IOP) less than 21 mm Hg and no clinical sign of corneal edema.Fifty-five eyes of 55 patients (30 congenital glaucoma and 25 controls) were examined (mean age = 16.6 ± 10.6 months; 20 female/ 35 males). There was no significant difference in age and gender between glaucoma patients and normal subjects. Mean IOP was higher in glaucomatous eyes (P = 0.02). Corneal diameter and axial length between glaucomatous eyes and controls were significantly different (P < 0.0001 for both). Central corneal thickness was significantly thinner in glaucomatous eyes (P = 0.01). There was a significant correlation between corneal diameter and central corneal thickness and also between central corneal thickness and axial length (r2 = 0.32 and r2 = 0.18, respectively; P < 0.0001 for both).Central corneal thickness was significantly thinner in children with congenital glaucoma. This finding may be another confounding factor when measuring IOP in those patients. Pachymetry should be considered during their examination.