X-ray contrast techniques were tested on the chick embryos in early periods of embryogenesis. For contrast stain, reagents with radiopacity in various concentrations were used: silver proteinate, eosin, Lugol’s solution (I2KI), phosphomolybdic acid and phosphotungstic acid under heating at 25 °C and 40 °C and exposure for 24 and 48 h. The use of silver proteinate, eosin and I2KI in various concentrations in the contrast of the chick embryo in the early period of embryogenesis did not make it possible to obtain microtomographic results that provide reliable microstructural analysis. The most optimal and effective method of embryo staining at the HH22–HH34 embryonic stages reliably determined the staining of 1% phosphotungstic acid at 40 °C heating and exposure for 24 h. Taking into account the size of the chick embryos and their structures at the HH22–HH34 embryonic stages, the features of the development, location of organs, and the minimum permissible parameters of microtomography for obtaining high-quality and reliable results were determined by the isometric spatial resolution of 8.87 μm, X-ray voltage 50 kV, X-ray current 500 μA, and the use of filters started from Al 0.5 mm. Microtomographic results were obtained, characterized by the appearance of the chick embryo at the HH22–HH34 embryonic stages, and they visualized the locations and structures of the chick embryo organs and provided calculation of their volume and X-ray density. The results of the work open up significant prospects for using the chick embryo at the early embryonic period of embryogenesis as an alternative model for screening teratogenicity.