Organoid cultures mimic the composition, structure, and function of the organ they derive from to a certain extent, providing more physiologically and biologically relevant results to humans than the currently used monolayer cell cultures and animal models. Organoids have been derived for several organs, from both pluripotent and adult stem cells, and are becoming more commonly used in different areas of research, including development, disease, and pharmacological studies. Their potential in genotoxicity assessment has been reported, although it is still at an early stage. Methods to assess gene expression changes, DNA damage, and metabolite formation have been used and are outlined here.