The present results support the idea of a shared genetic background between smoking and use of alcohol and cannabis. In conclusion, our data point to a genetic architecture of many common variants with very small individual effect sizes, influencing both smoking behavior and alcohol- and cannabis use. This analysis provides the first evidence that aggregated genetic risk factors are shared between substances. The finding that genetic variants have cross-substance effects is an important step towards understanding the common co-occurrence of the use of different substances. Our findings suggest that besides ‘substance-specific’ genes, we’ll also have to search for ‘general substance-use’ genes.