Premature ovarian failure (POF) is a complicated and heterogeneous disease. In majority of cases the underlying cause is not identified. Among the known causes, genetic aberration plays very important role. POF not only causes infertility, also adds the risk of osteoporosis and coronary heart disease because of the low level estrogen. The major therapy measures in present include hormone replacement therapy and infertility treatment with donated oocytes, but the effect is not ideal. To identify the genes of POF is the basis for treating and preventing this disease. A large number of candidate genes of POF are found on X chromosome and autosomes. The present paper reviewed the advance in mutation analysis on the candidate genes of POF, which is aimed to provide a basis to explore its molecular mechanism.