To find biomarkers for risk prediction of pancreatic cancer (PC), we evaluated the frequency of micronuclei (MN) in peripheral lymphocytes of 346 patients with PC and 449 healthy controls. The levels of baseline MN (mean ± standard error of micronucleated cells per 1000 binucleated cells) were significantly higher in patients (15.3 ± 0.3) than those in controls [9.7 ± 0.5; adjusted for body mass index (BMI), P < 0.001]. Using the median levels found in controls as the cut point, 78.9% of patients and 43.7% of controls had a higher frequency of MN. Logistic regression analysis with adjustment for known risk factors for PC showed that having a higher level of MN was significantly associated with increased risk of PC [odds ratio (OR): 8.32, 95% confidence interval (CI): 5.06-13.67, P < 0.001]; and the risk was much higher in men than in women [OR (95% CI): 14.19 (7.09-28.40) versus 4.19 (1.90-9.27)]. The level of MN was not associated with disease stage or resection status but was related to smoking status in men and to BMI in women among patients. The level of MN was higher in smokers (14.5 ± 0.6) than in nonsmokers (12.1 ± 0.6; P = 0.023) and in obese (25.3 ± 2.8) versus normal weight individuals (17.7 ± 0.8; P = 0.024). These data showed that elevated level of MN in peripheral lymphocytes was associated with increased risk of PC.