As one of the most common endocrine disorder, the etiology of PCOS remains incompletely unknown. However, family studies have showed that genetic basis is responsible for PCOS and that no single gene can explain this syndrome entirely [23,24,25]. It is reported that 40–80% of PCOS women are overweight or obese [26,27,28,29]. Therefore, based on the high prevalence of obesity in PCOS and the heritable of obesity [30], genes associated with obesity might play a role in pathogenesis of PCOS such as FTO gene. Recent years, many studies have been conducted to identify the relationships between FTO rs9939609 and PCOS susceptibility. However, the results were inconsistent, making these associations more indistinct. The current meta-analysis was aimed at clarifying the association of FTO rs9939609 and PCOS.

In our meta-analysis, we found that FTO rs9939609 polymorphism was associated with PCOS under different genetic models. This finding is consistent with the study by Li et al. They performed a two stage study involving 3599 PCOS and 3082 control subjects in Chinese population [14]. They found that rs9939609 polymorphism of FTO is associated with PCOS in Chinese women, no matter the PCOS women are obese or non-obese. This indicated that FTO might interact with PCOS directly. However, because of insufficient data, this potential interaction way can not be re-analyzed in our meta-analysis. Contrary to our result, a case-control study by Kim et al. observed that FTO polymorphisms of rs9939609 are not major determinants of PCOS. But for women with PCOS, the variant allele of FTO rs9939609 was associated with increased BMI, suggesting FTO polymorphism contributes to PCOS risk through affecting BMI indirectly [16]. Therefore, the associations among PCOS, BMI/obese and FTO polymorphism still remain indistinct. FTO might indirectly play a role in PCOS risk via BMI/obese. Also, FTO might contribute to PCOS by directly interacting or via the combined direct and indirect ways. More studies are needed to demonstrate it.

In subgroup analysis, the significant association between FTO polymorphism and PCOS was found not only in Caucasian but also in Asian, suggesting ethnicity was not the potential source of heterogeneity. Partly in line with our result, a case-control study by Cai et al. observed that FTO rs9939609 polymorphism (or its proxy) was associated with PCOS only in East Asians, but not in Caucasians [19]. In Caucasians subgroup of study by Cai et al., one of the two included studies was about FTO rs9939609 and another was about FTO rs8050136. So, we inferred this point might the source of different conclusion compared with our subgroup result.

Several limitations of this meta-analysis should be acknowledged. First, the number of studies included in our meta-analysis was relatively small, thus leading to smaller studies in subgroup analysis and weaken statistical power. Second, potential sources of heterogeneity in this meta-analysis should include other factors such as BMI, waist-to-hip ratio (WHR), obese. However, because of limited data, we could not explore these factors in current meta-analysis. Finally, it is well known that the etiology of PCOS involving in gene-gene, and gene-environment interactions. However these interactions could not be investigated in our meta-analysis due to insufficient information.