Objective To investigate the relationship between BRCA1 protein expression in lung cancer tissues and the effect of gemcitabine and Cisplatin based chemotherapy.Methods 80 cases of squamous cell carcinoma confirmed by pathology from May 2013 to May 2015 were selected, and treated with gemcitabine plus cisplatin chemotherapy and Ginseng and Astragalus assisted theropy.BRCA1 protein expression of all patients were detected, and relationship between the effect of chemotherapy and prognosis of patients with BRCA1 protein expression in lung cancer tissues were studied.Results In 80 cases, BRCA1 protein was positive in 40 cases, 40 cases were negative, CR 5 patients, PR 6 patients with BRCA1 positive expression, the remission rate was lower than the BRCA1 negative patients ( P <0.05 ) .80 cases of adverse reactions were seen as leukopenia, gastrointestinal symptoms (nausea and vomiting), abnormal liver function, BRCA1 expression of peripheral neurotoxicity, the incidence of complications in patients with positive expression were significantly higher than BRCA1 negative patients(P<0.05).N stage (P=0.03), BRCA1 gene (P=0.02) were independent risk factors of the prognosis of patients.Conclusion BRCA1 protein positive patients in lung cancer tissue had poor chemotherapy effect, more adverse reactions, and poor prognosis.