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Objective To analyze the relationship between single nucleotide polymorphisms (SNP) of Notch1 gene rs3124599 and susceptibility to lung cancer in patients with primary lung cancer. Methods A total of 78 patients with primary lung cancer (observation group) and 156 healthy subjects (control group) were enrolled. The morning venous blood of the two groups were taken (2 m L). DNA was extracted by phenol-chloroform extraction and Notch1 gene rs3124599 locus typing was analyzed by PCR-PFLPS technique. The clinical data of the two groups were collected. The correlation between various factors and susceptibility to lung cancer was evaluated by conditional logistic regression analysis. The interaction coefficient (γ) was used to evaluate the interaction between environmental factors and gene polymorphism. Results The distribution frequencies of Notch1 gene rs3124599 genotypes AA,AG,GG in the observation group were 25.6% (20/78),39.7% (31/78),and 34.6% (27/78),which were 37.2% (58/156),44.9% (70/156),and 17.9% (28/156) in the control group; the distribution frequencies of alleles A and G in the observation group were 45.5% (71/156)and 54.5% (85/156),respectively,which were 59.6% (186/312) and 40.4% (126/312) in the control group. The differences of the distribution of genotypes and alleles A and G between the two groups were statistically significant (χ2=6.518,3.987; all P < 0.05). The number of smoking,degree of smoking,and the family history of cancer in the observation group were higher than those in the control group (χ2= 23.890,5.647; P < 0.05). Conditional logistic regression analysis showed that individuals with rs3124599 GG genotype had an increased risk of lung cancer as compared with individuals with rs3124599 AA genotype (corrected OR = 1.596,95% CI: 1.058-2.429). The individuals carrying alleles G gene were 1.193 times more likely to develop lung cancer than those carrying A gene (95% CI: 1.132 to 2.501,P <0.05). The rs3124599 locus AG or GG genotype had positive interaction with smoking (γ = 2.296) and drinking (γ =1.130). When the rs3124599 locus AG/GG genotype was associated with a family history of the tumor,the risk of developing lung cancer increased (OR = 3.751,95% CI = 1.665-18. 034). Compared with rs3124599 genotype AA non-smokers,the risk of lung cancer in smokers or smokers carrying AG/GG increased by 4.495 times and 12.134 times,respectively. Conclusion The mutation frequency of allele G in Notch1 gene rs3124599 is higher in lung cancer patients. The allele G of the Notch1 gene rs3124599 (A/G) may be a risk factor for lung cancer,and it has an interaction with the patient’s family history of cancer and smoking history. [ABSTRACT FROM AUTHOR]