Background: The study examined the oral microbiota, physiological and immunological changes in patients using thermoplastic retainers during three months of use. Methods: The study included several steps. Firstly, 10 swabs were collected from the buccal and palatal surfaces of the teeth of the patients, approximately 2 mL of saliva was collected from the same patients and 2 mL of saliva was collected from 10 healthy people to measure the pH and secretory IgA level. This was followed by the isolation and identfication of the bacterial isolates in the patient samples. Then, isolate susceptibility toward chlorhexidine (CHX) and their adhesion ability to thermoplastic retainer surfaces was measured. In addition to that the study estimated the numbers of Lactobacillus and Streptooccus mutans colonies during three months and finally, a comparsion of pH acidity and IgA level between the patients and healthy people was performed. The results showed the predominant bacteria during the three months were Lactobacillus spp and Streptococcus spp followed by different rates of other bacteria. Raoultella ornithinolytica showed more resistance to CHX while Lactobacillus spp. showed more sensitivity. Streptococcus mutans colony levels were higher than Lactobacillus spp colonies during the three months, also S. mutans had the highest value in adherence to retainer thermoplastic. Finally, pH acidity showed a highly significant difference (p ≤ 0.05) in the third month, like IgA levels (p ≤ 0.05). Conclusions: According to the results obtained from the current study, the researchers noted that the thermoplastic retainers helped change the oral cavity environment.