The precise diagnostic testing is of high importance in fighting the coronavirus pandemic. While nasopharyngeal (NP) swab testing is currently the gold standard, the SARS-CoV-2 virus could be also detected in some other body fluids. In this study, we aimed to compare the SARS-CoV-2 RNA detection results, obtained using saliva samples and NP swab samples, collected from infected patients and healthy volunteers. Patients and Methods: A total of 111 individuals were enrolled in this study: 53 healthy volunteers, participating in routine testing and 58 COVID-19 patients. Diagnosis for both groups was confirmed using a set of diagnostic CE-IVD labeled RT-qPCR kits. Most of the saliva samples were collected within 48 hours after the NP swabs were taken. RNA was purified from saliva samples and analyzed using a laboratory-developed kit (Diagnolita). Detection results for both sample types were compared and analyzed in terms of result agreement, Ct variation, and quantity of internal control, as well as population analysis. Results: We found a good concordance between the NP swab and saliva samples. The positive percent agreement was 98.28% (CI 90.76-99.96%) and negative percent agreement was 98.11% (CI 89.93-99.95%). Additionally, we observed a statistically significant (p<0.05) and moderately strong (R = 0.53) correlation between Ct values in saliva and NP swab samples. The saliva collection method is more robust since the Ct variation of internal control ribonuclease P mRNA detection is lower in saliva samples. Conclusion: Saliva sample testing is a robust and reliable non-invasive alternative to the NP swab method for SARS-CoV-2 RNA detection, as well as a promising tool for COVID-19 screening.