The subgingival occurrence of yeasts and species of Enterobacteriacae and Pseudomonas was studied in 500 adults with severe periodontitis. All subjects had sites non‐responding or “refractory” to conventional periodontal therapy. Most subjects had received one or more courses of broad‐spectrum systemic antibiotics. Subgingival microbial samples were collected with paper points and transported in VMGA III. The bacterial samples were plated on enriched brucella blood agar and incubated anaerobically, and on TSBV, TBC, and Sabouraud agar, which were incubated in 10% CO2. Yeasts were speciated using the API 20C micro‐method system and the germ tube test (for Candida albicans). Enteric organism's and pseudomonads were speciated with the API 20E kit system. Yeasts, enteric rods and pseudomonads were subjected to antibiotic susceptibility testing. The occurrence of Actinobacillus actinomycetemcomitans, Bacteroides gingivalis, and Bacteroides intermedium was also determined in the patients studied. In the 500 periodontitis patients, yeasts were detected in 84 (16.8%), enteric rods or pseudo‐monads in 51 (10.2%), and both yeasts and enterics or pseudomonads in 6 (1.2%). Candida albicans comprised 83.3% of the isolated yeasts. Enterobacteriaceae averaged 21–39% of the cultivable flora in culture‐positive cases, with Enterobacter cloacae, Enterobacter agglomerans, Proteus mirabilis, Klebsietta pneumonias, and Klebsiella oxytoca being the most frequent species. Pseudomonas aeruginosa was isolated from 10 patients, averaging 23.4% of the cultivable subgingival flora. All Candida isolates, and 86–95% of the enteric rods and pseudomonads, were resistant to 1 μg/ml of tetracycline, penicillin G, and erythromycin. In patients positive for yeasts, enteric rods or pseudomonads, A. actinomycetemcomitans was isolated from about one‐fifth, B. intermedius from about one‐third, and B. gingivalis from 5% of the individuals. The present findings suggest that yeasts or enteric rods or pseudomonads occur in the subgingival flora of about one‐third of “refractory” adult periodontitis patients. We caution against using antibiotics without prior microbiological screening in treating this patient group.