To address the question if an altered oral microbiota is associated with atherosclerosis. Twenty patients suffering from atherosclerosis and 10 controls were recruited. Clinical oral, medical and laboratory investigations were performed. Oral bacteria were collected and 16S rDNA was sequenced following Single strand conformation polymorphism.(SSCP) Probing pocket depths in patients were significantly elevated. The oral microbiota of patients and controls were dominated by Fusobacterium (16%/17%), Streptococcus (21%/14%), Prevotella (10%/12%), Enterococcus (12%/12%), Porphyromonas (8%/7%), TM7 (0%/7%) and Veillonella (6%/7%). Differences in diversity were not significant between groups. The pathology of atherosclerosis may not be related to significant qualitative changes of the oral microbiota.