In patients with autoimmune hepatitis (AIH), osteoporosis represents a common extrahepatic complication, which we recently demonstrated by an assessment of areal bone mineral density (aBMD) via dual-energy X-ray absorptiometry (DXA). However, it is well established that bone quality and fracture risk does not solely depend on aBMD, but also on bone microarchitecture. It is currently not known whether AIH patients exhibit a site-or compartment-specific deterioration in the skeletal microarchitecture. In order to assess potential geometric, volumetric, and microarchitectural changes, high-resolution peripheral quantitative computed tomography (HR-pQCT) measurements were performed at the distal radius and distal tibia in female patients with AIH (n=51) and compared to agematched female healthy controls (n=32) as well as AIH/primary biliary cholangitis (PBC) overlap syndrome (n=25) and PBC alone (PBC, n=36). DXA at the lumbar spine and hip, clinical characteristics, transient elastography (FibroScan) and laboratory analyses were also included in this analysis. AIH patients showed a predominant reduction of cortical thickness (Ct.Th) in the distal radius and tibia compared to heathy controls (p<0.0001 and p=0.003, respectively). In contrast, trabecular parameters such as bone volume per tissue volume (BV/TV) did not differ significantly at the distal radius (p=0.453) or tibia (p=0.508). Linear regression models revealed significant negative associations of Ct.Th with age (95% CI:-14 to-5 µm / year, p<0.0001) but not liver stiffness, cumulative prednisolone dose (even after an adjustment for age) or disease duration. The duration of high dose prednisolone (≥7.5mg) was negatively associated with trabecular thickness (Tb.Th) at the distal radius but none of the other microarchitectural parameters. No differences in bone microarchitecture parameters between AIH, AIH/PBC and PBC could be detected. In conclusion, AIH patients showed a severe age-dependent deterioration of the cortical bone microarchitecture, which is most likely the major contribution to the observed increased fracture risk in these patients.