The Nos3-knockout mouse, deficient for endothelial constitutive nitric oxide synthase (NOS3), is affected by a reduction in the number and weight of the embryos and constitutes a good model for some features of preeclampsia and intrauterine growth retardation (IUGR). Deficiencies in conceptus growth and survival may result from factors inherent in the embryo itself or from deficiencies in uterine function. In the current study, we aimed to determine the effects of embryonic genotype independently of maternal genotype, which can affect uterine environment. Therefore, by using magnetic resonance imaging (MRI), we characterized the phenotypes of NOS3-defective (Nos3^−/−; n = 6), normal wild-type (Nos3 ^/ ; n = 5), and heterozygous (Nos3 ^/−; n = 16) mouse fetuses. All of them were littermates obtained by breeding heterozygous mice (Nos3 ^/−); therefore, the maternal genotype was the same for all the fetuses. At Day 13.5 (i.e., Theiler stage TS 21–22), females were anesthetized and scanned with three-dimensional MRI. Analysis of the different measurements of the embryos and the gestational annexes showed no significant differences between Nos3 ^/ and Nos3 ^/−; however, there was a trend toward larger sizes in Nos3 ^/ , and values in Nos3^−/− were significantly smaller than in Nos3 ^/ and Nos3 ^/−. The reduction in the crown-rump length of Nos3^−/− reached 12% when compared to Nos3 ^/ (P < 0.05); the effect was higher for head measurements (16% for occipito-snout length and biparietal diameter, P < 0.05 for both) and trunk diameter (17%, P < 0.05). Overall, the maximum area of fetuses in longitudinal planes decreased 27% (P < 0.05) when comparing Nos3^−/− to wild-type Nos3 ^/ . Finally, Nos3^−/− showed a reduction of 29% in the maximum thickness of the placenta, which may be related to the appearance of IUGR due to compromised nutritional delivery to the fetus.