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Importance: Owing to infrastructural and population characteristics, the prison setting is at increased risk for transmission of SARS-CoV-2 and for severe clinical outcomes. Because of structural and operational reasons, research in prison settings is challenging and available studies are often monocentric and have limited temporal coverage; broader-based research is necessary. Objectives: To assess the extent and dynamics of the COVID-19 pandemic within the prison system of a large Italian region, Lombardy, and report the infection prevention and control measures implemented. Design, Setting, and Participants: This repeated cross-sectional study was carried out from March 1, 2020, through February 28, 2021 (first wave, March-June 2020; second wave, October 2020-February 2021) in the prison system of Lombardy, which includes 18 detention facilities for adults. All incarcerated persons and the prison staff of the penitentiary system of the Lombardy region participated in the study. Exposures: The main exposures of interest were the weekly average number of incarcerated individuals placed in quarantine in single or shared isolation rooms, the rate of sick leave by symptomatic and asymptomatic prison staff reported to the prison occupational medicine department on a weekly basis, and the level of overcrowding. Main Outcomes and Measures: The primary outcome measures were weekly COVID-19 crude case rates, weekly test positivity rate, and the relative risk of acquiring the infection for prison staff, incarcerated persons, and the general population. Results: The study population comprised a mean of 7599 incarcerated individuals and 4591 prison staff. Approximately 5.1% of the prison population were women; demographic characteristics of the prison staff were not available. During the study, COVID-19 occurred in 1564 incarcerated individuals and 661 prison staff. Most of these cases were reported during the second wave (1474 in incarcerated individuals, 529 in prison staff), when stringent measures previously enforced were relaxed. During both epidemic waves, incarcerated individuals and prison staff had a higher relative risk for COVID-19 infection than the general population during both the first wave (incarcerated individuals: 1.30; 95% CI, 1.06-1.58; prison staff: 3.23; 95% CI, 2.74-3.84) and the second wave (incarcerated individuals: 3.91; 95% CI, 3.73-4.09; prison staff: 2.61; 95% CI, 2.41-2.82). Conclusions and Relevance: The findings of this study suggest that the prison setting was an element of fragility during COVID-19 pandemic, with a high burden of COVID-19 cases among both the incarcerated individuals and prison staff. The prison setting and prison population need to be included and possibly prioritized in the response during epidemic events.