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Purpose: To investigate the pathophysiology of punctal stenosis based on histopathological features, and to assess the correlation between histopathological findings and treatment outcomes in primary punctal stenosis., Methods: A total of 43 eyes of 34 consecutive patients with primary punctal stenosis were included in this prospective study. Punctum specimens obtained by rectangular three-snip punctoplasty (TSP) were examined based on the multilayered structure of the epithelium and subepithelial histopathology. The correlation between the histopathological findings and treatment outcomes was evaluated., Results: A total of 61.8% of the patients were female and had an average age of 62.4 (41-81) years. Based on the histopathological examination, all 43 puncta consisted of non-keratinized stratified squamous epithelia. Subepithelial pathology demonstrated inflammation in 10 puncta (23.3%), fibrosis in 19 puncta (44.2%) and both inflammation and fibrosis in 11 puncta (25.6%). There was a moderate relationship between the presence of subepithelial fibrosis and symptom duration ( r  = 0.4, p  = 0.03). The surgical success was 88.4% at the mean of 12.4 ± 3.5 months follow-up. The surgical success was clinically lower in the puncta with exhibited fibrosis, although it was not statistically significant ( p  = 0.6)., Conclusion: Although the findings for almost all punctum specimens were consistent with fibrosis, inflammation or both, subepithelial fibrosis was detected as the most common histopathological feature. Clinically lower surgical success rates in puncta exhibiting fibrosis may be associated with a longer duration of symptoms and excessive postoperative healing response.