Prevalence of oral cancer is relatively increasing in Yemen in recent years, which is ascribed to Qat with other carcinogens. Since the establishment of a simple and reliable method for the detection of oral cancerous and precancerous lesions is essential, exfoliative cytology (EC) was applied to a case-control study to appraise the presence and severity of oral epithelial atypia in 300 subjects (150 were Qat chewers and 150 were non-Qat users) without prior knowledge of the subjects' Qat exposure. Ten patients with oral squamous-cell carcinoma (OSCC) were included as internal controls. Cytological atypia and hyperkeratosis were demonstrated in six and 24 subjects, respectively, and could not be ascertained in the remaining 294 and 276 correspondingly. All of the 30 (six atypia and 24 hyperkeratosis) were among the 150 Qat chewers. Cytological atypia was found in all the 10 control cases with OSCCs (eight with severe degree and two with mild atypia). For the Qat among those with atypia and hyperkeratosis, the adjusted OR and the 95% confidence level were found to be 1.6 (0.8-7.2) and 3 (10.1-21.9), respectively. In view of these findings, we suggest the use of EC for detection and assessment of oral cytological atypia. Qat use contributes to the occurrence of cytological atypia that might develop to oral precancerous or cancerous lesions.