In the current study, we show that in NSCLCs treated with pembrolizumab, elevated nonsynonymous mutation burden strongly associates with clinical efficacy. Additionally, clinical efficacy correlates with a molecular signature characteristic of tobacco carcinogen–related mutagenesis, certain DNA repair mutations, and the burden of neoantigens. The molecular smoking signature correlated with efficacy, whereas self-reported smoking status did not, highlighting the power of this classifier to identify molecularly related tumors within a heterogeneous group.