The secretions of certain cytokines, chemokines and growth factors are triggered by orthodontic appliances, which often affect the remodelling of periodontal tissues. Critical cumulative forces are applied by various types of orthodontic appliances to the periodontium. The secretion of such molecules is probably responsible, through molecular and cellular communications, for the optimal resorption of hard tissues in the periodontal setting, which therefore enables the coordination of multiple movements of tooth. This study assessed and compared a wide range of cytokines, cellular marker analysis and defensins present in the saliva samples of human subjected to orthodontic treatment with two different treatment modalities, i.e., conventional lingual and labial fixed orthodontic appliances. A total 40 samples of saliva were obtained, of which 20 were treated with traditional lingual appliances and 20 were treated with labial fixed appliances. After 21 days of treatment, all salivary samples were collected from the subjects. In order to analyse a broad range of soluble cytokine levels in saliva by flow cytometry, a bead-based immunoassay was performed. Cell surface markers were analysed by flow cytometry. Protein levels of saliva for defensins were quantified by ELISA. Non-significant differences were observed in the cytokine levels in the saliva except for the significant effects for CCL2, IL-17A and IL-6. Cellular markers CD45 and CD326 showed high percentage in conventional lingual samples. Defensin levels were found to be lower in conventional lingual patients. Subjects with conventional lingual appliances had significantly higher salivary protein levels of IL-1β, CCL2, IL17A, and IL-6, higher CD45+ and CD326+ cells and lower defensin levels than subjects with fixed labial appliances. The current study provided a clear basis for the development of innovative methods to aid in the improvement of various procedural treatments and orthodontic equipment of next generation.