BACKGROUND: In the context of the COVID-19-pandemic, mortality and incidence are key determinants to assess the transmission dynamics and the resulting potential threat. Systematic microbiological monitoring of deaths provides a fundamental basis to particularly assess underrecording of community-acquired mortality. It should be further elucidated whether a death cohort of previously unreported cases may be structurally different from the cohort of officially registered cases. METHODS: A systematic reverse transcription (RT) qPCR testing for SARS-CoV‑2 infections from nasopharyngeal swab samples was carried out. A representative sample of corpses from crematoria and the Institute of Legal Medicine of the Federal State of Hamburg were included. A comparative analysis of primarily reported and unreported fatalities in an 8‑week period after occurrence of the first pandemic-related deaths in Hamburg was performed. RESULTS: A total of 1231 deaths were included, all of which were previously unsuspicious for SARS-CoV‑2 infection. Thereof 29 cases of previously unknown infections were recorded. In the first phase of the pandemic, incidental findings predominantly occurred among younger people from domestic environments with unclear or unnatural manner of death at the Institute of Legal Medicine. Over time, incidental findings investigated at the crematoria increased, mostly related to nursing home residents. The overall cohort showed no significant sociodemographic differences to a comparative collective of known SARS-CoV‑2-associated deaths. Primarily unreported cases showed a significantly lower proportion of COVID-19 as the underlying cause of death. CONCLUSION: A systematic PCR-based monitoring of deaths allows a more targeted detection and classification of SARS-CoV‑2 positive cases. A preventive contribution can be made by disclosing unreported pandemic-related cases of death.