Strict control of dental plaque accumulation remains the cornerstone of successful maintenance of the treated patient. However, some recurrences of periodontitis appear to take place despite good oral hygiene habits. A proportion of these are likely due to qualitative features of the periodontal microbiota rather than merely increased mass. Microscopic as well as cultural monitoring of qualitative features of the periodontal microbiota may be helpful in detecting critical changes. This review presents some of the research findings that provide a rationale for microbiological monitoring. Some of the advantages as well as difficulties encountered with these procedures are discussed.