Abstract Background So far knowledge about undocumented migrant health status is poor. The objective of this study is to compare patterns in causes of death between undocumented migrants and legal residents, of both migrant and non-migrant origin. Method Using cause-of-death data, we compared undocumented migrants with Belgian residents and documented migrants through logistic regression analyses. Results This study shows that male undocumented migrants have a significantly higher risk of death from cardiovascular diseases compared to male Belgian residents (OR: 1.37) and documented migrants (OR: 2.17). Male undocumented migrants also have an increased risk of dying from external causes of death compared to documented migrants (OR: 1.93). Furthermore, we found a lower risk of suicidal death in undocumented migrants compared to Belgian residents (OR men: 0.29, OR women: 0.15). Conclusions We found important differences in underlying causes of death between undocumented migrants and residents in Belgium. These findings urge us to claim improved healthcare provision for undocumented migrants in Belgium. Trial registration Medical ethics committee UZ Jette, Brussels, Belgium – Registration date: 18/05/2016 – Registration number: B.U.N. 143201628279.