Objective: The aim of this study was to use cerebrospinal fluid (CSF) cytology to give undiagnosed patients admitted to the hospital with severe neurological symptoms and without any anti-tumor treatment history a definitive diagnosis. Further, the aim was to explore the relationship between the frequency of gene mutations and mortality on the incidence of CSF metastasis in advanced non-small-cell lung cancer (NSCLC). Materials and methods: 30 patients diagnosed with NSCLC through CSF cytology were retrospectively analyzed. We analyzed 30 CSF metastasis patients and a control group of 20 advanced NSCLC patients without CSF metastasis. Results: 30 patients were diagnosed with CSF metastasis using CSF cytology and immunocytopathology. The frequencies of EGFR mutations and ALK fusion in the CSF metastasis group were higher than they were in the non-CSF metastasis group (80% and 50% respectively, P<0.05). The incidence of CSF metastasis with gene mutations was higher than it was with wild-type genes (70.6% and 37.5%, P<0.05), OR 4.0 (95% CI 1.14 similar to 13.99). The median survival time of the CSF metastasis group was 4.8 months (95% CI 4.2 similar to 5.3). However, the median survival time in the non-CSF metastasis group was 9.2 months (95% CI 3.3 similar to 15.1). The mortality of the CSF metastasis group (n=13, 43.3%) was significantly higher than it was in the non-CSF metastasis group (n=6, 30%). Conclusions: CSF metastasis in NSCLC patients has a higher frequency of gene mutations and mortality. EGFR mutation and ALK fusion patients have a higher incidence of CSF metastasis. EGFR mutations and ALK fusion may promote CSF metastasis and may be a predictor of prognosis in NSCLC patients.