Background: The homeless population of France has increased by 50% over the last 10 years. Studies have shown that homelessness is associated with a high risk of premature death. The aim of this study was to estimate the number of homeless deaths in France between 2008 and 2010, using a reproducible method. Methods: We used the capture-recapture method to estimate the number of homeless deaths in France using two independent sources. An associative register of homeless deaths was matched with the national exhaustive database of the medical causes of death, using several matching approaches based on various combinations of the following variables: gender, age, place of death, date of death. Results: The estimated number of homeless deaths between 2008 and 2010 was 6730 (95% CI: [4381–9079]), a number greatly underestimated by the two sources considered separately (less than 20%). Conclusions: In the absence of a register of the homeless deaths, the capture-recapture method provides an order of magnitude for evaluation of the resources that may be allocated by policy makers to manage the issue. Based on common and routinely produced databases, this estimate may therefore be used to monitor the mortality of the homeless population. Further studies about homeless mortality, particularly on the lead causes of deaths, are needed to manage this issue and to implement strategy to decrease the number of homeless deaths.