To identify the genetic factors influencing complex diseases is a challenging problem. With the development of several technologies, such as large-scale genome sequencing, gene chips and mass spectrometry, and the successful completion of the first phase of International HapMap Project, it is feasible to explore the associations between hundreds of polymorphisms in the human genome, even the whole genome, and complex diseases in populations with large number of samples. The present paper briefly describes the results of the International HapMap Project, the merging whole-genome association study, and some new methods applicable to data including multiple loci.