Background: The Covid-19 pandemic has led to substantial and unexpected increases in morbidity and mortality in France. Vulnerable populations housed in accommodation centres have a greater risk of infection because collective housing and their dependence on social support services mean it is more difficult to apply preventive measures. They are also at greater risk of developing severe forms of Covid-19 and waiting longer before seeking healthcare (for Covid-19 or other) treatment. We aimed to identify the factors associated with SARS-CoV2 infection in the most vulnerable populations in the city of Marseille. Methods: The study sample comprised users of various services provided by the association AAJT in Marseille, France, some presenting symptoms suggestive of Covid-19 and others not. All had routine health surveillance provided by AAJT's dedicated healthcare team between March 2020 and May 2020. Using univariate and multivariate analyses, we studied the influence of several variables on morbidity associated with Covid-19. Results: The study included 64 participants, 29 of whom tested positive for Covid-19 and 35 control subjects. Median age was 21.16 years old. Individuals in the 'Covid-19 case' group (p < 0.005)which included persons testing positive and those suspected of being infectedwere younger. The study sample's male/female ratio was seven. In our multivariate analyses, living in a shared apartment and poor adherence to social distancing measures were factors associated with Covid-19 infection. Furthermore, mental health problems-such as anxiety disorder-were very frequent in the study sample. Conclusions: Allocating more and specific housing units to structures providing accommodation services to the most vulnerable people would seem to be a decisive factor in controlling the spread of SARS-CoV2, and deserves more attention from public authorities.