Acquired resistance is a common occurrence among patients with oncogene-driven non-small-cell lung cancer receiving targeted therapies. Monitoring of circulating tumour DNA in liquid biopsy samples provides an appealing, minimally invasive method of monitoring for acquired resistance in this setting. However, research into detecting mechanisms of acquired resistance in liquid biopsy samples has thus far been limited by various challenges. In this Perspective, the authors describe the available data on detecting mechanisms of acquired resistance to targeted therapies in patients with non-small-cell lung cancer, as well as the various challenges to progress, such as a lack of a consensus definition of acquired resistance, and other inconsistencies in the approach to detecting and investigating these alterations.