Background: Prenatal rat embryo exposure to retinoid induces some malformations in various organs, the most active and teratogenic metablolite is all-trans-retinoic acid (atRA). The teratogenic effects of some drugs can be prevented by the application of antioxidant drugs and stimulation of the maternal immune system. Also, quercetin, a naturally occurring flavonoid has excellent antioxidant properties. Therefore, in this study, the prophylactic effect of quercetin on teratogenic effects of atRA was evaluated.Materials and Methods: In this experimental study, 40 pregnant rats were divided into 7 groups. Control group received normal saline and test groups received dimethylsulfoxide (DMSO), quercetin (75 mg/kg), quercetin (200 mg/kg), atRA (25 mg/kg), atRA (25 mg/kg) plus quercetin (75 mg/kg) and atRA (25 mg/kg) plus quercetin (200 mg/kg), intraperitoneally at 8-10th days of gestation. Fetuses were collected at 20th day of gestation and after determination of weight and length; they were stained by Alizarin red- Alcian blue method.Results: Cleft palate, exencephaly and spina bifida incidence were 30.76%, 61.53% and 30.76% range in group which received only atRA. Cleft palate, exencephaly and spina bifida incidence were 11.11%, 16.66% and 5.55% in group which received atRA plus quercetin (75 mg/kg). However, cleft palate, exencephaly and spina bifida incidence were 10.52%, 10.52% and 0% in group which received atRA plus quercetin (200 mg/kg). The means of weight and length of fetuses from rat that received atRA plus quercetin (75 mg/kg) were significantly greater than those received only atRA.Conclusion: It is concluded that quercetin decreased teratogenicity induced by atRA, but this subject needs more detailed evaluation.