Genotoxicity testing is a vital aspect of the safety assessment of new products (e.g., pharmaceuticals, foodstuffs, industrial chemicals). The ability of an agent to induce DNA damage is linked to long-term cancer risk as DNA damage is known to drive genome instability and carcinogenesis. There is much focus these days on the 3Rs (replacement, reduction, and refinement of animal testing), and in vitro tests are being sought to replace animal approaches. These new approach methodologies (NAMs) include the use of 3D human tissue models. Liver 3D models are particularly valuable as liver enzyme metabolism is sometimes difficult to recapitulate in vitro, and 3D liver models are known to express liver-specific enzymes at higher levels than 2D liver cells. Hence, the 3D liver models are more representative of human physiology. We present here detailed methodologies using 3D liver cell models to study DNA damage induction, specifically using the well-regarded micronucleus approach. We offer insights into the methods used and adaptations for nanomaterial assessment and other modifications possible with these approaches.