BACKGROUND: Droplet digital PCR (dd-PCR) is a recently developed method with improved reliability and sensitivity. The present study compared RT-qPCR and dd-PCR techniques for detecting the EGFR G719S and T790M mutations in formalin-fixed, paraffin-embedded (FFPE) tissue samples of lung cancer and cervical cancer. STUDY DESIGN: We collected 54 tumor samples from cervical cancer patients and 60 lung cancer patients with stage. The expression of EGFR in FFPE samples was detected through immunohistochemistry assay, and the EGFR mutation status was determined by DNA extraction from FFPE slides followed by droplet digital PCR. RESULTS: The expressions of EGFR were significantly increased in FFPE samples of both lung cancer and cervical cancer. On the other hand, the EGFR G719S and T790M mutations were detected in lung cancer tissue but not detected in cervical cancer by dd-PCR method. The results of the dd-PCR analysis were confirmed by Scorpion amplification refractory mutation system (ARMS) assay. CONCLUSION: The establishment of highly sensitive droplet digital PCR detection is a new method for studies on FFPE samples. The EGFR genotype assay results supplemented clinical information and could facilitate therapeutic approach design. © Science Printers and Publishers, Inc.