BACKGROUND: The characteristics of the corneal endothelium in patients with/without pseudoexfoliation syndrome (PEX) with senile cataract in Paraguay are unknown. METHODS: Endothelial density, mean coefficient of variation (%) in cell size and mean cell hexagonality (%) were measured using automated specular microscopy. Multivariate general linear model analysis was used to determine the effect of age, gender and PEX on endothelial characteristics. Analysis of variance tests analysed the effect of age on endothelial variables without regard to PEX status. Categories of <2000 and > or =2000 cells/mm(2) were compared in the presence/absence of PEX using age as covariate to calculate odds ratios for corneal decompensation. RESULTS: Out of 468 eligible patients, 51 were excluded. Sixty-one patients had PEX. Unadjusted mean endothelial cell density was 2451 cells/mm(2); cell size coefficient of variation was 34.3; and the mean percentage of hexagonal cells was 57.7. Adjusting for age, only the mean difference between the groups with and without PEX for endothelial cell density was significant (PEX = 2315, no PEX = 2482, P = 0.002). Of the total study population, at-risk endothelial cell densities were found in 46 eyes (11%); and 13 (28%) of those were found to have PEX. When PEX was present, the calculated odds ratio for corneal decompensation following surgery was 1.90 after adjustment for age. CONCLUSIONS: Endothelial cell density data were consistent with published literature. Because Paraguay has a high prevalent of PEX, it is suggested that specular microscopy screening be carried out for all patients scheduled for intraocular surgery where feasible.