The aim of the study was to evaluate the biochemical and molecular variables in the epiglottis, tongue, and hard palate and compare with healthy controls in oral squamous cell carcinoma (OSCC). Methods: This was a prospective and cross-sectional study conducted at Malla Reddy Medical college and tertiary care hospitals in Hyderabad with individuals having oral malignancies (OM). 60 adults aged ≥ 18 years, diagnosed with OM (20 each of tongue, epiglottis, and hard palate) were included in the study. Those who had cancer at more than one area were excluded from the study. Blood samples were collected from each participant and used for testing the expression of biochemical and molecular markers in oral squamous cell carcinoma. They were analysed by the genomic sequencing method. Student ‘t’ test and one-way ANOVA with Bonferroni's t-test was used for statistical analysis. Results: Biomarkers and proteins such as Schiff bases, diene conjugate, triene conjugate, haptoglobin (Hapto), transferrin (Transf), β2-microglobulin, ceruloplasmin, complement 4 components (C4c), complement 3 component (C3c), Transthyretin (TTR), lipid bound sialic acid (LBSA) and total sialic acid (TSA) in HPV positive (+ve) and negative (-ve) samples were expressed significantly compared to control (p < 0.001). The difference between them was not significant even though most of the studied markers were highly expressed in all three types of malignancy compared to the control Conclusion: The levels of oxidative parameters, protein metabolites, biochemical markers and the conjugate were elevated in tongue, hard palate and epiglottis compared to the normal control. However, the above parameters did not change in tongue hard palate and epiglottis showing cancer can cause similar type of effect. The assessment of these parameters may help in early detection of oral malignancies.