The method of contrasting with iodine ions was developed to obtain high-resolution 3D images of large biological specimens using a synchrotron X-ray microtomography unit. It was shown that the samples (late mouse embryos) treated with 50% Lugol solution with addition of 25% ethanol for 48 h followed by a 48-h washout in phosphate buffered saline had maximum contrast and lowest compression artifacts. Processing of samples by this protocol allowed detecting zones of active proliferation. Incubation of brain samples for 120 h in 7.6% meglumine/sodium diatrizoate without washout ensured the best contrast during myelin identification.