The Healthcare Associated Infections Annual Report 2020 reflects the work undertaken on healthcare associated infection (HCAI) prevention and containment of antimicrobial resistance (AMR) during 2020. Data are provided for common HCAIs, which are an important cause of severe illness, death, and higher treatment costs. This year the report also includes analysis of hospital onset COVID-19 and the impact of COVID-19 on other Scottish national surveillance systems. The global pandemic brought unique challenges during 2020. Antimicrobial Resistance and Healthcare Associated Infection (ARHAI) Scotland within NSS have been a key part of the national COVID-19 response to the pandemic. This report details the progress made by ARHAI Scotland to support the reduction of HCAIs in NHS Scotland as well as providing data to inform local and national HCAI prevention activities.