A series of 993 subgingival microbial samples sent to a diagnostic microbiology laboratory included 196 samples that could be identified as compatible with a clinical diagnosis of refractory or recurrent periodontitis. In descending order of prevalence the associated microbiota included Bacteroides forsythus (84%), spirochetes (83%), motile rods (76%), Fusobacterium species (68%), Porphyromonas gingivalis (63%), Campylobacter rectus (47%), Capnocytophaga species (38%), Prevotella intermedia (23%), Peptostreptococcus micros (18%), Actinobacillus actinomycetemcomitans (16%), Candida (14%), enteric rods (9%), Staphylococcus species, not including aureus (5.6%). Eikenella corrodens (3%), Staphylococcus aureus (1.5%), and Enterococcus species (< 1%). Antibiotic resistance to tetracycline, penicillin G, or metronidazole was particularly noticeable for enteric rods, Fusobacterium species, Capnocytophaga species, Staphylococcus, and Actinobacillus actinomycetemcomitans. It was largely absent for Campylobacter rectus. No antibiotic sensitivity data were obtained for Porphyromonas gingivalis or Bacteroides forsythus, as these species were detected by immunofluorescence. The results indicate that a substantial number of microorganisms associated with refractory periodontitis are variably resistant to commonly-used antibiotics. Diagnostic microbiology must be considered an essential adjunct to the therapist faced with periodontal lesions refractory to conventional treatment.