Genome-wide association studies (GWAS) have quickly become the norm in dissecting the genetic basis of complex diseases. Family-based association approaches have the advantages of being robust to possible hidden population structure in samples. Most of these methods were developed with limited markers. Their applicability and performance for GWAS need to be examined. In this report, we evaluated the properties of the family-based association method implemented by ASSOC in the S.A.G.E package using the simulated data sets for the Framingham Heart Study, and found that ASSOC is a highly useful tool for GWAS.