Smoothened (SMO) inhibitors are under clinical investigation for the treatment of several cancers. Vismodegib is approved for the treatment of locally advanced and metastatic basal cell carcinoma (BCC). Most BCC patients experience significant clinical benefit on vismodegib, but some develop resistance. Genomic analysis of tumor biopsies revealed that vismodegib resistance is associated with Hedgehog (Hh) pathway reactivation, predominantly through mutation of the drug target SMO and to a lesser extent through concurrent copy number changes in SUFU and GLI2. SMO mutations either directly impaired drug binding or activated SMO to varying levels. Furthermore, we found evidence for intra-tumor heterogeneity, suggesting that a combination of therapies targeting components at multiple levels of the Hh pathway is required to overcome resistance. Display omitted •Recurrent mechanisms reactivate the Hh pathway in SMO inhibitor-resistant BCC•Drug-binding pocket and activating SMO mutations reduce sensitivity to vismodegib•Downstream SUFU variants co-occur with alterations predicted to increase GLI2 levels•A relapsed tumor can harbor multiple resistance mechanisms Sharpe et al. identify SMO mutations in the binding pocket for SMO inhibitors or that constitutively activate SMO in vismodegib-resistant basal cell carcinoma. They demonstrate that a single relapsed tumor can harbor clones with different resistance mutations.