To determine the effects of fixed orthodontic appliances on periodontal health and microbiological composition of subgingival dental plaque. This prospective longitudinal self-controlled study was conducted on 32 adolescents (13 males, 19 females), who were scheduled for fixed orthodontic treatment between 2002 and 2005. Dental plaque accumulation, gingival inflammation and pocket probing depth were measured at the mesio-vestibular angle of the examined group of teeth followed by collection of subgingival dental plaque samples in the same points. These periodontal indices and microbiological parameters were determined prior to the placement of fixed appliances and 1, 3 and 6 months after the beginning of orthodontic treatment. All values of both clinical and microbiological parameters started to increase after the placement of fixed appliances. Maximum values were reached 3 months after fixed appliance placement followed by their decrease in the last registration period of 6 months after the placement of fixed appliances. Treatment with fixed appliances in adolescents may transitionally increase the values of all periodontal indices and stimulate the growth of periodontopathogenic bacteria, but without destructive effects on deep periodontal tissues.