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The coronavirus disease 2019 (COVID-19) has a great impact on healthcare workers (HCWs) that includes negative mental health outcomes, such as post-traumatic stress, anxiety and depressive symptoms. In this cross-sectional study, we report on mental health outcomes among HCWs in Cyprus. Data were collected between 3 May and 27 May 2020, with the use of an online questionnaire that included demographics (sex, age, occupation, education, work sector, years of work experience), the 9-item Patient Health Questionnaire (PHQ-9) which assesses depressive symptoms, the Impact of Events Scale Revised (IES-R), which measures post-traumatic stress disorder (PTSD) symptoms, and the-10 item Perceived Stress Scale (PSS-10) which quantifies stress responses. Participants (42% physicians, 24% nurses, 18% physiotherapists, 16% classified as "other") were 58% of female gender and aged 21–76. A total of 79 (18.6%) and 62 HCWs (14.6%) reported clinically significant depressive (PHQ-9 ≥ 10) and post-traumatic stress (IES-R > 33) symptoms respectively. Nurses were more likely than physicians to suffer from depression (adjusted prevalence ratio 1.7 (1.06–2.73); p = 0.035) and PTSD (adjusted prevalence ratio 2.51 (1.49–4.23); p = 0.001). Even in a country with a rather low spread of the COVID-19, such as Cyprus, HCWs reported a substantial mental health burden, with nurses reporting increased depressive and PTSD symptoms compared to other HCWs.