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BACKGROUND: Orthodontic tooth movement is a complex process involving a number of inflammatory and anabolic/catabolic pathways. Further, successful treatment depends on proper timing of orthodontic measures with regard to patient’s growth spurt. Saliva analysis has emerged as a non-invasive collection method to track biomarkers relevant to both tooth movement biology and growth prediction. The aim of the present study was to analyze changes in tooth movement and assess relationships with salivary levels of alkaline phosphatase, IGF-1, TGF-β1, testosterone, BMP-2, BMP-4, and BMP-9t. METHODS: Twenty seven healthy patients (17 females, 10 males) with a mean age of 13.3 years, undergoing orthodontic treatment with a non-extraction treatment plan were selected for the study. Height, weight, and other demographic features were recorded; maxillary and mandibular alginate impressions were obtained, and 10 mL saliva samples were taken at the initial visit (T0), after 4 weeks (T1), 3 months (T2), and then at 3-month intervals (T3, T4, T5). Casts were made from alginate impressions. Little’s Irregularity Index, intercanine widths, intermolar widths, arch lengths, and tooth widths were measured. Saliva samples were analyzed for the concentrations of alkaline phosphatase, IGF-1, TGF-β1, testosterone, BMP-2, BMP-4, and BMP-9 by multiplex immunoassay and/or ELISA. Data were analyzed using correlation coefficients and ANOVA. RESULTS: Over the six timepoints, there were statistically significant changes in the level of testosterone (p < 0.05) and Little’s Irregularity Index (p < 0.01), with the most significant changes occurring at the beginning of treatment (T0 to T1). Statistically significant correlations (p < 0.05) were observed between testosterone and height/weight, intercanine width and intermolar width, BMP-4 and intercanine/intermolar width, alkaline phosphatase and testosterone, alkaline phosphatase and TGF-β1, and among the BMPs. CONCLUSION: The changes in Little’s Irregularity Index reflects successful progress of the orthodontic treatment. The correlations observed among the various salivary concentrations suggest a number of further directions for study.