Biomarker testing in patients with advanced stage non-small cell lung cancer provides essential information that can be used to select the most appropriate therapy. The regular updates of guideline recommendations reflect the growing number of biomarkers that must be assessed, and as such signal the shift from single-gene assays to more comprehensive genomic profiling using next-generation sequencing modalities. Cytology and small biopsy specimens have proven to be more than adequate substrates for these types of ancillary molecular testing; however, other alternative testing substrates are beginning to emerge. These include so-called liquid biopsies as well the supernatant fluid from cytology specimens, both of which have demonstrated promise for use in the clinical realm. This review will briefly cover the current state of non-small cell lung cancer biomarker testing in the United States, with a focus on these novel nonconventional substrates that are increasingly being incorporated into testing paradigms.