Objectives: The SARS-CoV-2 coronavirus is a major public health problem for a number of reasons, one of which is the constant mutation of the viral genome and the consequent emergence of new variants. In the period in which this research was done, Omicron became the dominant variant in the world. In this study, we researched the prevalence of variants of interest in patients tested at University hospital centre Zagreb, compared the relationship between variants between patients who are not hospitalized, emergency and hospital patients, and patients treated in the COVID department, and compared RT-PCR testing results with SARS-CoV-2 genome sequencing results for the purpose of identifying variants. Study Design: The study was organized as a cross-sectional study. Patients and Methods: Samples of patients tested at University hospital centre Zagreb by routine processing, RT-PCR testing for E gene, N gene and ORF1ab gene was used. After the positivity was determined, part of the samples was sent for genome sequencing, and part was retested by another RT-PCR test to identify variants. The obtained results were compared, and the prevalence of SARS-CoV-2 variants among patients was investigated. Results: The results of the research showed that the dominant SARS-CoV-2 variant in October was Delta, and in the following months, by the end of April 2022, this variant almost completely disappeared from the patient population, and the Omicron variant became dominant. It was initially a BA.1 variant but was later replaced by a BA.2 variant. Patients who are not hospitalized were tested the most, in whome the most common variant was BA.2, while in patients admitted via emergency department, the Delta variant was the most common. Samples of patients treated in COVID department and other departments were most commonly identified as Omicron (BA.1 and BA.2). Comparison of sequencing results and RT-PCR testing showed a significant difference in matching. SUMMARY 22 Conclusion: The data obtained in this study show that the prevalence of SARS-CoV-2 variants in patients tested at the University Hospital Center Zagreb follows global epidemiological trends, and that the final confirmation is obtained by genome sequencing.