Diagnosis and treatment in dentistry are based on clinical examination of thepatients. Given that the major oral diseases are of microbial biofilm etiology,it can be expected that performing microbiological analysis on samplescollected from the patient could deliver supportive evidence to facilitate thedecision-making process by the clinician. Applicable microbiological methodsrange from microscopy, to culture, to molecular techniques, which can beperformed easily within dedicated laboratories proximal to the clinics, such asones in academic dental institutions. Periodontal and endodontic infections,along with odontogenic abscesses, have been identified as conditions in whichapplied clinical microbiology may be beneficial for the patient. Administrationof antimicrobial agents, backed by microbiological analysis, can yield morepredictable treatment outcomes in refractory or early-occurring forms ofperiodontitis. Confirming a sterile root canal using a culture-negative sampleduring endodontic treatment may ensure the longevity of its outcomeand prevent secondary infections. Susceptibility testing of samples obtainedfrom odontogenic abscesses may facilitate the selection of the appropriateantimicrobial treatment to prevent further spread of the infection.