This study screened FOXO3 coding regions for mutations in a sample of 114 Chinese women with premature ovarian failure and discovered six novel single-nucleotide variants: c.71C>A (p.Pro24His), c.140C>T (p.Pro47Leu), c.184G>A (p.Asp62Asn), c.1652C>T (p.Ser551Phe), c.1697C>G (p.Gly566Ala) and c.1185G>A (silent). The nonsynonymous single-nucleotide variants, c.71C>A (p.Pro24His), c.140C>T (p.Pro47Leu), c.184G>A (p.Asp62Asn), c.1652C>T (p.Ser551Phe) and c.1697C>G (p.Gly566Ala), were not detected in any of 100 controls. These missense mutations might cause abnormal oocyte apoptosis and primordial follicle activation, thereby adversely affecting early follicle depletion in the ovary.