A cross-sectional study examining oral manifestations was carried out in HIV-infected patients of a general HIV-specialized unit to provide prevalence data on oral lesions and periodontal diseases. The occurrence of oral lesions was correlated with demographic and clinical characteristics, immunologic and virologic parameters. Among 139 patients 86% presented any oral lesions with a prevalence of 76% of any periodontal diseases. Most periodontal lesions were classified as conventional gingivitis (28%) or periodontitis (30%). Dental plaque formation was associated with a higher prevalence of periodontal diseases (p = 0.01) and periodontal inflammation scores were higher in patients with more reduced CD4-counts (p = 0.03). Prevalence for HIV-specific oral lesions was 29% with a proportion of 9% of linear gingival erythema (LGE), 3.6% of necrotizing and ulcerative gingivitis (NUG) or periodontitis (NUP), 7% of oral candidiasis, 3.6% of oral hairy leucoplakia (OHL) and single other lesions. HIV-specific lesions (NUG/NUP, oral candidiasis and OHL) were found predominantly in patients with advanced immunosuppression and elevated viral load. Compared with data of oral diseases of the pre-HAART era prevalence of HIV-specific lesions was markedly reduced. Especially frequently known lesions such as oral candidiasis and OHL were less common seen. We noticed a shift of prevalence towards periodontal diseases. Lack of oral hygiene determined by plaque formation and reduced CD4-counts with pronounced periodontal inflammation can be seen as risk factors for periodontal disease. Overall high prevalence of manifestations underlines the importance of oral examination for the general practitioner and visits by oral specialists should become a routine procedure in HIV-patients care.