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Background Cryopreserved embryo transfer has become indispensable in reproductive technology. More and more children are conceived from frozen-thawed embryo transfer (FET). The risk of birth defects associated with frozen-thawed embryo transfer has been evaluated and conflict results are obtained. The aim of this study was to compare the rate of major malformations in children conceived from cryopreserved embryos with that of children from fresh embryos. Methods A retrospective analysis was performed on children conceived from frozen-thawed embryos and fresh embryos between January 2005 and December 2008 at the Reproduction Center of the Third Hospital, Peking University.The major malformation rates were compared between two groups for all children, as well as singletons or twins,separately. The frequencies of different subtypes of malformations classified according to different organ system were also compared.Results Thirty-four of 3125 children from cryopreserved embryos had a major malformation. The malformation rate was 1.09%, which was comparable to that for children after fresh embryos transfer (1.53%(55/3604), OR:0.71, 95% CI; 0.46-1.09). The malformation rate was also similar when the analysis was limited to children from cryopreserved embryos resulted from in vitro fertilization (IVF)(1.39%)and fresh IVF(1.3%). However, children from cryopreserved embryos resulted from intracytoplasmic sperm injections (ICSI) had much lower malformation rate than from fresh ICSI(0.63% vs.1.83%, OR: 0.34, 95% CI: 0.16-0.75). No difference was found in the incidence of major malformations in singletons from cryo ICSI (0.73%) and fresh ICS1(1.9%), or from cryo IVF(1.49%) and fresh IVF(1.67%). Similar malformation rate was found in multiples from cryo ICSI(0.52%) and fresh ICSI(1.76%), or cryo IVF(1.30%) and fresh IVF(0.90%). The distribution and risk of the subtype of malformations, such as cardiovascular, gastrointestinal, neural tube, urogenital,usculoskeletal and facial abnormalities was not different between the cryo group and fresh group. Conclusions The major malformation rate is similar between fetuses/children conceived from cryopreserved embryos and those from fresh embryos. Large prospective and long-term follow-up studies are needed to get exact results concing the birth defects of the children b after cryopreserved embryos.