Liquid biopsy is currently approved for management of epidermal growth factor receptor ()-mutated non-small-cell lung cancer (NSCLC) patients. However, one unanswered question is whether the rate of cell-free DNA (cfDNA)-negative samples is due to technical limitations rather than to tumor genetic characteristics. Using four microsatellite markers that map specific chromosomal loci often lost in lung cancer, we conducted a pilot study to investigate whether other alterations, such as loss of heterozygosity (LOH), could be detected in -negative cfDNA. We analyzed -mutated NSCLC patients ( = 24) who were positive or negative for mutations in cfDNA and compared the results with a second cohort of 24 patients bearing -mutated cancer, which served as a representative control population not exposed to targeted therapy. The results showed that in -negative post-tyrosine-kinase-inhibitor (TKI) cfDNAs, LOH frequency was significantly higher than in both pre- and post-TKI -positive cfDNAs. By contrast, no association between status in cfDNA and number of LOH events was found. In conclusion, our study indicates the feasibility of detecting LOH events in cfDNA from advanced NSCLC and suggests LOH analysis as a new candidate molecular assay to integrate mutation-specific assays.