Introduction: In 2007, the mandatory BCG vaccination requirement was suspended and replaced by a recommendation to vaccinate children at high risk of tuberculosis. Since then, it has no longer been possible to easily estimate BCG vaccination coverage in mainland departments, with the exception of Île-de-France. The objective of this study was to estimate BCG vaccination coverage among children at high risk of tuberculosis in the Bas-Rhin department and its districts. Methods: This cross-sectional survey was conducted in Bas-Rhin among children aged 3 to 4 years enrolled in the youngest class of public preschools during the 2012–2013 school year. The sample was selected using a two-stage stratified sampling design based on two criteria; regression estimates were adjusted according to the sampling design. Results: The response rate was 82.1% (2,560 children in the 102 schools surveyed); 35.1% of the children were at high risk for tuberculosis: their BCG vaccination coverage was 72.3%, with significant variations across districts—low (<50%) in Saverne and Haguenau, and high (>80%) in Strasbourg and Molsheim. The healthcare provider who administered the vaccination was primarily the family physician. Conclusion: BCG vaccination coverage varied considerably by district. Identifying the areas with the lowest vaccination coverage should enable better targeting of future vaccination promotion efforts.