Background To investigate corneal endothelial cell density in eyes with primary pterygium. Methods A retrospective study was conducted to compare endothelial cell density between 1,565 patients with primary pterygium and 3,448 patients without pterygium. Then a prospective study was designed to confirm the findings of the retrospective study in 95 patients with unilateral primary pterygium. Results In the retrospective study, the mean endothelial cell density in eyes with primary pterygium was significantly lower (2,454 +/- 303 cells/mm(2)) than those in eyes without pterygium (2,525 +/- 312 cells/mm(2), p < 0.0001). However, the difference was not as high as previously reported (71 cells/mm(2), 2.9 per cent). In the prospective study, there was no significant difference in mean endothelial cell density in eyes with unilateral primary pterygium (2,480 +/- 263 cells/mm(2)) and the contralateral eyes with no pterygium (2,527 +/- 277 cells/mm(2), p = 0.20). There was also no significant difference in hexagonality (p = 0.10) or co-efficient of variation of size (p = 0.15) of corneal endothelial cells between eyes with pterygium and the contralateral eyes with no pterygium. Conclusion Primary pterygium may not be associated with a decrease in endothelial cell density in our study population of rural Chinese patients.