Objective This study aimed to investigate the prognostic value of viral load detected in the saliva of COVID-19 patients in the early stage of infection. Study design Oro-nasopharyngeal swab and saliva samples were collected from all patients simultaneously in the early stage of COVID-19. Viral loads were determined by extracting viral RNAs from saliva samples of patients whose ONP swabs were positive for SARS-CoV-2 by RT-qPCR. The demographic information, comorbidities, cycle threshold values, and one-month clinical courses were recorded and compared. Results The patients' clinical course was evaluated for one month; 56% of patients had mild disease, 26.4% had moderate disease, 9.6% had severe disease, and 8% had a critical/mortal disease. The average cycle threshold values of SARS-CoV-2 in saliva and ONP samples were measured as 22.28 and 24.19, respectively. Cycle threshold value of saliva was found to be significant in predicting disease severity (Eta coefficient 0.979). A statistically significant relationship was found between the disease's severity and the mean of ONP samples’ Ct-values (p < 0.05). Gender, age, body mass index, and co-morbidities were compared with the severity of the disease; no statistically significant difference was found. Conclusion Viral load detected in saliva in the early period of COVID-19 infection may have a prognostic value in showing the disease's course in patients over 45-year-old. Saliva is an easily obtainable, reliable material for COVID-19 screening.