This study aimed to evaluate the effect of using an inferior or superior conjunctival autograft in primary pterygium surgery on the postoperative ocular surface. Forty eyes of 40 patients who underwent pterygium surgery with autograft were included in the study. Cytological cell counts were performed on samples taken from the bulbar conjunctiva by impression cytology before and 1 year after the operation. Schirmer 1 test score, lissamine green conjunctival staining score, tear film break-up time (TBUT), and fluorescein corneal staining scores were evaluated. The pain levels of the patients were evaluated with visual analog scale at postoperative 1 day and 1 week. Corneal and conjunctival staining, TBUT, and Schirmer test results demonstrated significant improvement in all patient groups after surgery, but there was no difference between groups (p>0.05). In both preoperative and postoperative impression cytology, the number of goblet cells in the inferior bulbar conjunctiva was higher than in the superior bulbar conjunctiva (p<0.001), while there was no such difference in epithelial cell or mucin staining. There were no significant cytological changes postoperatively in either group (p>0.05). Pterygium surgery with autografting improved tear function tests regardless of graft location. Goblet cell count was higher in the inferior bulbar conjunctiva than in the superior bulbar conjunctiva in both postoperative and preoperative impression cytology. However, there was no significant difference in postoperative epithelial and goblet cell counts or mucin staining between the groups before and after surgery. We think that using the inferior bulbar conjunctiva is an appropriate choice in cases where the superior conjunctiva cannot be used as a graft or when future glaucoma surgery is possible.