Background/aim: The aim of this study was to investigate cytomorphological and cytopathological changes in oral exfoliated smears collected from immunosuppressed patients with Behçet's disease (BD) using stereological methods. Materials and methods: For cytomorphometric analysis, mucosal cell smears were obtained from the buccal mucosa and the floor of the mouths of BD patients treated with immunosuppressive drugs and from healthy volunteers. All mucosal smears from the patients and the healthy volunteers were stained using the Papanicolaou method and examined cytopathologically under light microscopy and cytomorphologically via the stereological nucleator method. Results: The cytomorphological analysis revealed 3 types of mucosal cells, with numbers of particularly pink cells lower in the aphthous areas of the patients with BD compared to the healthy controls (P < 0.05). The nuclear volumes (NVs) and cytoplasmic volume (CVs) were significantly higher in the BD patients (P < 0.05), but the NV/CV ratio was higher only in the drug-use patient groups (P > 0.05). There was lower apoptotic activity in the nondrug-use patients with BD and in the immunosuppressive-taking BD patients. Conclusion: The findings suggest that quantifiably morphological and morphometric changes in oral mucosa can be detected by stereological techniques. Changes in these parameters may indicate malignant transformation in the oral mucosa.