The issues complicating the analysis of complement proteins in PCOS are that the obesity and insulin resistance with accompanying inflammation are so highly correlated to PCOS that statistical regression adjustment for BMI over-adjusts PCOS effects; therefore, in this study, a comparison between obese PCOS and PCOS subjects who were nonobese, non-insulin-resistant, and without increased systemic inflammation was undertaken using a comprehensive panel of complement proteins to determine whether the complement factor proteins are independently associated with PCOS. This evidence concerns the gene VTN and Insulin resistance.