Introduction: The purpose of this study was to compare and evaluate salivary microbial levels and periodontal status in patients using a fixed lingual retainer, a removable vacuum-formed retainer, or a Hawley retainer after orthodontic treatment with fixed appliances. Methods: Forty-five patients who finished their orthodontic treatment with fixed appliances and were about to start the retention phase were randomly divided into the following 3 groups of 15 individuals each: the fixed lingual retainer group, the vacuum-formed retainer group, and the Hawley retainer group. Periodontal measurements, such as the plaque index, gingival index, probing depth, and bleeding on probing, were obtained at the following 4 time points: at debonding (T0) and 1 week (T1), 5 weeks (T2), and 13 weeks (T3) after debonding. Saliva samples were collected 3 times in total: at T0, T2, and T3. A quantitative analysis for Streptococcus mutans and Lactobacillus casei was performed with the use of real-time polymerase chain reaction. The Kruskal-Wallis test and 1-way analysis of variance were used for the statistical comparisons of the groups. Results: No statistically significant difference in salivary S mutans and L casei levels was found among the 3 groups (P >0.05). They showed no statistically significant differences in plaque index, gingival index, bleeding on probing, and probing depth values (P >0.05). All periodontal parameters showed statistically significant decreases from T0 to T3 in all 3 groups (P <0.001). The S mutans and L casei levels were decreased significantly from T2 to T3 in the lingual retainer and Hawley retainer groups, whereas they decreased significantly from T0 to T3 in the vacuum-formed retainer group. Conclusions: Fixed and removable orthodontic retainers do not differ in salivary S mutans and L casei levels and periodontal status. With all retainers, regardless of whether they are fixed or removable, oral hygiene improved after orthodontic treatment with fixed appliances.