The purpose of this study was to develop a site-specific sampling method that could give representative and quantitative results for defined areas of the oral mucosa and would be easy to use. Two site-specific sampling methods (swab and filter paper imprint) were compared. The filter paper sampling method was developed for this study. Samples were collected from 14 volunteers. All samples were cultured under aerobic and anaerobic conditions. The number of viable bacteria and yeasts was determined and expressed per unit area. The filter paper recovered a significantly higher number of colony types of bacteria compared to the swab sample. Both collected a large number and variety of different oral microbes. The filter paper sampling method could be the optimal technique for quantitative site-specific oral mucosal samples and is highly suitable for both culture-based and non-culture-based identification of oral microbes. © Springer-Verlag 2008.