Introduction: Most individuals with SARS-CoV-2 experience mild symptoms, however, many can experience a severe form of the disease, which can also be fatal. Several studies have associated serum pro-inflammatory cytokines with disease severity. However, very few have associated early cytokine changes, following viral infection of the nasopharyngeal region, with disease severity. Therefore, our study aimed to associate changes in viral loads and the expression of various cytokines in nasopharyngeal samples with COVID-19 disease severity.Material and Method: A total of 118 SARS-CoV-2 nasopharyngeal samples in the viral transfer medium were collected. The samples were characterized as mild and severe, based on the WHO criteria, and qPCR was performed to determine the viral loads and also evaluate the expression of eight cytokines (IL-1, IL-2, IL-4, IL-6, IL-10, IFN-γ, TGF-β1 and TNF-α) expression in the mild and severe group. Subsequently, appropriate statistical tests were applied to determine the differential expression of cytokines in the mild and severe groups and to correlate the viral loads and cytokine expression with disease severity.Results: Out of 118 nasopharyngeal samples, 71 were characterized as mild, while 47 as severe. The mean viral load between the mild and severe groups was comparable (mild group: 27.07I 5.22; severe group: s 26.37 n7.89). Analysis of the cytokines showed the expression of IL-2, IFN- γ and TNF-α to be significantly higher in the severe groups as compared to the mild group. Further, we also observed a significant positive correlation between all the cytokines in the severe group.Conclusion: We found IL-2, TNF-α, and IFN-γ expression to be significantly higher in severe cases as compared to mild. The increased expression of pro-inflammatory cytokines in the nasopharyngeal milieu may be considered as biomarkers for disease severity in COVID-19 positive patients.