BACKGROUND: Patterns of sickness absence shed useful light on disease occurrence and illness-related behaviours in working populations. METHODS: We analysed prospectively collected, pseudonymized data on 959 356 employees who were continuously employed by National Health Service trusts in England from 1 January 2019 to 31 July 2020, comparing the frequency of new sickness absence in 2020 with that at corresponding times in 2019. RESULTS: After exclusion of episodes directly related to COVID-19, the overall incidence of sickness absence during the initial 10 weeks of the pandemic (March-May 2020) was more than 20% lower than in corresponding weeks of 2019. Trends for specific categories of illness varied substantially, with a fall by 24% for cancer, but an increase for mental illness. A doubling of new absences for pregnancy-related disorders during May-July of 2020 was limited to women with earlier COVID-19 sickness absence. CONCLUSIONS: Various factors will have contributed to the large and divergent changes that were observed. The findings reinforce concerns regarding delays in diagnosis and treatment of cancers and support a need to plan for a large backlog of treatment for many other diseases. Further research should explore the rise in absence for pregnancy-related disorders among women with earlier COVID-19 sickness absence.