Topical antimicrobial treatment is appearing as a means of therapy in patients with advanced periodontal disease. The purpose of the present study was to examine the occurrence of doxycycline resistant bacteria in subgingival plaque and oral cavity after local administration of doxycycline. Five patients with advanced marginal periodontitis were scaled, and one approximal pocket in each patient was additionally treated with locally delivered doxycycline. Microbiological samples were obtained from the test site, a contralateral control site and tongue and tonsils before treatment and 3, 13, 26 and 52 weeks after treatment. The occurrence and morphological distribution of doxycycline resistant bacteria was determined after anaerobic cultivation on enriched tryptic soy agar with and without doxycycline incorporated. At the test site and on tongue and tonsils the percentage of doxycycline resistant bacteria increased from less than 1% before treatment to 22% and 35%, respectively, immediately after treatment, but decreased again at week 13. At the control site no increase was observed. Gram-positive cocci constituted the majority of doxycycline resistant bacteria at all 3 sampling sites (73-94%). The morphological distribution of resistant bacteria was not affected by the doxycycline therapy. Thus, local doxycycline therapy resulted only in a transient increase in resistance in the oral microflora.