Single nucleotide polymorphisms (SNPs) are the most common sources of variation between humans. As a kind of new genetic marker, SNPs are used extensively in gene location, clone and genetic polymorphisms. Specially, as diagnostic markers, the genetic SNPs play an important role in preventive medicine. In recent years, with the development of human genome project, millions of SNPs are reported and freely available in public databases. The rapid increase of SNP number and the development of detection methods for SNPs provide probability for the analysis of cancer susceptibility. In this review, we described main methods for high-throughput SNP analysis technologies. We summarized the application of SNPs analysis by large-scale analytic technologies in cancer susceptibility, the current understanding of SNP analysis in the different populations, tumor susceptibility genes and individual cancer susceptibility, as well as the obstacles in discovering the relationship between SNP analysis and cancer susceptibility underlying complex human traits.