Purpose: The aim of this study was to assess the role of PCR in conjunctival swab in the diagnosis of coronavirus disease 2019 (COVID-19) disease. Patients and methods: This is a prospective cross-sectional study that included 50 patients with confirmed COVID-19 infection with and without conjunctivitis. Reverse transcriptase PCR was done for all conjunctival swabs to detect the presence or absence of coronavirus RNA. Results: The mean age of the patients was 51.9±0.8 years, with 19 (38%) patients having conjunctivitis and 31 (62%) patients without conjunctivitis. The mean days since the onset of COVID symptoms was 9.5±0.7 days. Fever was present in 48 (96%) patients and respiratory symptoms were present in 49 (98%) patients. Positive, weak positive, and negative reverse transcriptase PCR of conjunctival swabs were detected in nine (18%), seven (14%), and 34 (68%) patients, respectively. Conclusion: There were low viral RNA loads in the conjunctival swab. So, its analysis cannot offer an opportunity to confirm the diagnosis of COVID-19 infection.