This report presents the clinical results three months after application of minocycline microspheres as an adjunct to mechanical treatment of incipient peri-implant infections compared to adjunctive treatment employing 1% chlorhexidine gel application. Sixteen patients in the minocycline group and 14 in the chlorhexidine group completed the study. Each patient had one or more implants with probing depth > or = 4 mm combined with bleeding and/or exudate on probing and presence of putative pathogenic bacteria. At baseline, patients were randomly assigned to minocycline or chlorhexidine treatment. Follow-up examinations were carried out after 10, 30, 60 and 90 days. The combined mechanical/antimicrobial treatment for the chlorhexidine group did not result in any reduction in probing depth and only limited reduction of bleeding scores. The adjunctive use of minocycline microspheres, on the other hand, resulted in improvements in both probing depths and bleeding scores. For the deepest sites of the treated implants, mean probing depth was reduced from 5.0 mm to 4.1 mm. The reductions in bleeding scores, although greater than for the chlorhexidine group, were modest. Thus, the question as to what extent the combined mechanical/minocycline treatment could be considered adequate for the treated lesions remains to be answered. The present short-term findings, however, encourage further studies with longer observation intervals on adjunctive use of minocycline microspheres in the treatment of periimplant lesions.