The cause of spontaneous abortion of normal conceptuses remains unknown in most cases. The study was aimed to reveal the latent abnormalities by using a large collection of embryo images from a magnetic resonance imaging (MRI) database and novel phase-contrast radiographic computed tomography (PXCT). MRI from 1,156 embryos between Carnegie stage (CS) 14 and CS23 from the Kyoto Collection were screened by using the volume of the liver as the target organ. Embryos with liver volumes >= 2 SD above or below the mean for the stage of development were screened and examined precisely on MRI. Embryos with potentially abnormal livers were further analyzed by using PXCT. Liver abnormality was detected in all 7 embryos in the extra-small liver group and in 2 of 8 embryos in the extra-large liver group. The abnormalities in the extra-small liver group consisted of hepatic agenesis (2 embryos), hepatic hypogenesis (4), and liver lobe defect (1). Among the 7 extra-small liver group, 2 had only liver abnormalities and 5 exhibited complications in other organs. Of the 2 embryos in the extra-large liver group, one had only a single liver abnormality and the other had a morphologically abnormal liver with complications in other organs. Most of such liver abnormality cases are not survive, as liver function becomes essential. The prevalence of liver malformations in CS18 and CS21 in the intrauterine population of externally normal embryos is approximately 1.7%. The present study is the first step toward the elucidation of the latent abnormalities resulting in spontaneous abortion in externally normal embryos. Anat Rec, 299: 824, 2016. (c) 2015 Wiley Periodicals, Inc.