In February 2020, Italy became the epicenter for COVID-19 in Europe, and at the beginning of March, the Italian Government put in place emergency measures to restrict population movement. Aim of our analysis is to provide a better understanding of the epidemiological context of COVID-19 in Italy, using commuting data at a high spatial resolution, characterizing the territory in terms of vulnerability. We used a Susceptible-Infectious stochastic model and we estimated a municipality-specific infection contact rate () to capture the susceptibility to the disease. We identified in Lombardy, Veneto and Emilia Romagna regions (52% of all Italian cases) significant clusters of high , due to the simultaneous presence of connections between municipalities and high population density. Local simulated spreading in regions, with different levels of infection observed, showed different disease geographical patterns due to different values and commuting systems. In addition, we produced a vulnerability map (in the Abruzzi region as an example) by simulating the epidemic considering each municipality as a seed. The result shows the highest vulnerability values in areas with commercial hubs, close to the highest populated cities and the most industrial area. Our results highlight how human mobility can affect the epidemic, identifying particular situations in which the health authorities can promptly intervene to control the disease spread.