Introduction/Aims Limb girdle muscular dystrophy type R9 (LGMDR9) is characterized by progressive weakness of the shoulder and hip girdles. Involvement of proximal extremity muscles is well-described whereas information about axial muscle involvement is lacking. It is important to recognize the involvement of axial muscles to understand functional challenges for the patients. The aim of this study was to investigate the involvement of axial and leg muscles in patients with LGMDR9. Methods This observational, cross-sectional study investigated fat replacement of axial and leg muscles in 14 patients with LGMDR9 and 13 matched, healthy controls using quantitative MRI (Dixon technique). We investigated paraspinal muscles at three levels, psoas major at the lumbar level, and leg muscles in the thigh and calf. Trunk strength was assessed with stationary dynamometry and manual muscle tests. Results Patients with LGMDR9 had significantly increased fat replacement of all investigated axial muscles compared with healthy controls (P < .05). Trunk extension and flexion strength were significantly reduced in patients. Extension strength correlated negatively with mean fat fraction of paraspinal muscles. Fat fractions of all investigated leg muscles were significantly increased versus controls, with the posterior thigh muscles being the most severely affected. Discussion Patients with LGMDR9 have severe involvement of their axial muscles and correspondingly have reduced trunk extension and flexion strength. Our findings define the axial muscles as some of the most severely involved muscle groups in LGMDR9, which should be considered in the clinical management of the disorder and monitoring of disease progression.