Pseudoexfoliation (PEX) syndrome is one of the leading causes of secondary open angle glaucoma and blindness. This study explored whether in PEX eyes, preoperative changes in corneal endothelial cell morphology might be a risk factor for postoperative corneal decompensation. Methods: One hundred twenty six eyes of 69 preoperative cataract patients (43 males, 26 females) were enrolled in this cross-sectional study from the Ophthalmology Department at Sultan Qaboos University Hospital between 2003-2005. All patients were subjected to confocal biomicroscopy. Results: The mean age of patients with PEX eyes was 63.2 years. One hundred and eight (85.7%) eyes with PEX had endothelial cell counts within the normal range (1650-3500/mm²). The qualitative morphology of the endothelium of PEX corneas was highly abnormal in term of polymegathism and pleomorphism. Twelve eyes had endothelial cell counts higher than normal for that age group. Only 6 eyes had endothelial cell counts lower than normal. The mean value for the pleomorphism was found to be significantly lower than normal and for polymegathism significantly more than normal. The relationship between pleomorphism and polymegathism was stronger for males than for females and stronger for patients under 60 years than patients over 60 years. The same relationship between pleomorphism and polymegathism showed a stronger relationship for the glaucoma group as compared to the non-glaucoma group. Conclusion: This study revealed that corneal decompensation in PEX eyes can occur in presence of abnormalities in polymegathism and pleomorphism, even when the endothelial cell counts may be normal.