During 2003, a total of 258 new patients with oral soft tissue lesions were admitted at the Stomatology Service of the Department of Oral Surgery and Stomatology at the University of Berne. For the present study, 185 patients with clinically and histopathologically verified diagnoses were included. The following data was collected: prevalence of oral mucosal lesions, distribution of benign, precancerous and malign lesions in different age groups, and the concordance of the referral with the working diagnosis at the Stomatology Service. The most frequent pathological soft tissue findings were fibrous hyperplasias (n = 44) and oral lichen planus (n = 30). Precancerous lesions were present in 41 cases (30 patients with oral lichen planus, eleven oral leukoplakias), and ten patients had oral malignomas. Most lesions were found in patients between the age of 40 and 60 years. The referral diagnosis concurred in 36.6% (n = 67) of the cases with the definite diagnosis before initiation of treatment, the working diagnosis in 70% (n = 128) of the cases. Therefore, it can be concluded that a specialised Stomatology Service serves as a center of competence due to large numbers of patients/cases seen and treated, and the resulting high level of clinical experience of the staff. Moreover, it is important in the primary diagnosis of oral squamous cell carcinoma, in collaboration with the referring dentist in private practice.