Microscopic computed tomography (microCT) has been recently applied to morphological evaluation of mouse embryos with or without congenital malformations, and 3-dimensional (3D) digital images of the whole embryo can be obtained. In the present study, the authors report a modified, rapid technique of 3D embryonic microCT without processing with osmium tetroxide. Normal embryonic days 10.5 to 11 mouse embryos, as well as those with craniofacial anomalies treated with teratogens, were examined. After fixation, we processed the embryo samples with hexamethyldisilazane, instead of highly toxic osmium tetroxide in the original method. Our protocol enabled clear 3D craniofacial imaging of the normal and anomalous mouse embryos within a short period of 20 minutes or 1 hour. In addition, some anatomical landmarks were clearly detected in the reconstituted craniofacial section images. Our present data suggest a possible role of microCT for high-throughput morphological screening of the mouse embryos with craniofacial anomalies.