Two counterpart paintings, the Assumption of the Virgin Mary and the Transfiguration of Christ on the Mount from the property of the National Heritage Institute, Regional Heritage Administration in Kroměříž, were subjected to conservation/restoration and a detailed material investigation. Findings obtained from an X-ray photograph created by a novel method, an X-ray microradiography with a large-screen pixel detector, have been employed in the course of the investigation. Our research confirmed that the paintings differ in painter’s style as well as in their material composition and the history of secondary interventions (damage and subsequent repairs). Any connection between the paintings could also be completely excluded based on the composition of the ground layers, which have a direct relationship to the provenance of the paintings.