Background: EGFR tyrosine-kinase inhibitors have shown efficacy in non-small-cell lung cancer (NSCLC) with specific EGFR mutations. The impact of KRAS and BRAF mutations on therapeutic response remains under evaluation. The study aimed validating the use of mutation detection kits in a routine laboratory. Methods: The mutation status of the EGFR, KRAS and BRAF genes, previously determined by Sanger sequencing, was analyzed with two approaches, pyrosequencing (Therascreen® Pyro® kits) and allele specific amplification (Cobas® mutation tests). A set of 70 DNAs from NSCLC tissue samples was selected and harboured 7 EGFR, 3 KRAS and 4 BRAF mutations. Results: The Cobas® kit missed one EGFR and all BRAF mutations, and the Therascreen® kit missed one KRAS and 2 BRAF mutations. The Cobas® kit run in a one-step procedure, while the Therascreen® Pyro® kit included several manual steps, a plate’s format change and a final analysis on a separate computer with specific software, allowing access to each experimental result. The Cobas® kit did not give the exact nature in case of mutation. Both kits have thus similar ability to detect mutations. Conclusions: The Cobas® kit appears suitable for a high-throughput use in a medical laboratory but the synthetic final report presents a limit for full quality of the process. No kit presently integrates flexibility regarding the constant evolution in the set of mutations to be detected.