A recent genome-wide association study showed that the rs9939609 polymorphism in the fat mass and obesity-associated (FTO) gene was associated with body mass index (BMI)/obesity in Europeans. Subsequently, several studies have investigated the association between FTO polymorphism and cancer risk. However, the results have been inconsistent. In this study, a meta-analysis was performed to clarify the association between FTO polymorphism and cancer risk. Published literature from PubMed and Embase databases were retrieved. Pooled odds ratio (OR) with 95 % confidence interval (CI) was calculated using fixed-effects model. A total of 13 studies involving 16,277 cases and 31,153 controls were identified. The results suggested that FTO rs9939609 polymorphism was not significantly associated with the increased risk of cancer (OR = 1.01, 95 %CI 0.98-1.04), with the exception that a statistically significant association was found for pancreatic cancer (OR = 1.10, 95 %CI 1.03-1.19). No publication bias was detected (Begg's test: P = 0.760; Egger's test: P = 0.553). Our meta-analysis indicated that there was no association between FTO rs9939609 polymorphism and the increased risk of cancer, although this polymorphism was marginally associated with pancreatic cancer. However, the conclusion should be made with caution since most included studies did not take BMI/obesity into account.