Since 2020, the COVID-19 (Coronavirus Disease 2019) has quickly become a worldwide health problem. Ophthalmologists must deal with symptoms as well. For the positive detection in the conjunctival sac swab in COVID-19 patients hospitalized in Slovakia during March 2021 in four hospital centers, we used a test based on a polymerase chain reaction (PCR). In a group of 484 patients, 264 males (55%) and 220 females (45%) with clinical symptoms were identified with COVID-19 as a clinical diagnosis. The PCR test swab results from the conjunctival sac taken on the same day were positive in 58 patients (12%), 31 males (with a mean age of 74.6 ± 13.59 years) and 27 females (with a mean age of 70.63 ± 14.17 years); negative in 417 patients (86%); and 9 patients (2%) had an unclear result. The cycle threshold values comparing the nasopharynx and conjunctiva were also different in the group of all patients divided by age and gender. In COVID-19 patients the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was detectable using PCR test in the nasopharynx but also in the conjunctival sac swab, where the positivity rate was only 12%.