Little is known about the skeletal muscle characteristics (fibre type proportion and size, location of nuclei, presence of fat infiltration) in children with liver disease with radiologically determined myopenia (low muscle mass). During liver transplantation (LTx) surgery, biopsies from the rectus abdominis muscle were collected. Muscle fibre types (I, I/IIA, IIA, IIA/X, IIX) and CSA index (µm/m2) were determined using immunofluorescence staining. Triacylglycerol (TAG) and phospholipid content of muscle was determined using gas chromatography. Myopenia was defined using study-specific cut offs (skeletal muscle index <-2SD) from age-sex matched healthy control scans. Myopenia was prevalent in 41% of children. Children also had a high prevalence of high muscle adiposity (37%). Children with myopenia were older (8.4 vs. 0.7 yrs; p<0.001), had smaller total (median 595 vs. 844 µm/m2; p=0.04) and hybrid IIA/X (612±143 vs. 993±341 µm/m2; p=0.04) muscle fibre size index, lower prevalence of type I fibres (53 vs. 64%; p=0.01) and higher prevalence of type IIA/X hybrid fibres (median 7.5 vs. 0%; p=0.04). Children with myopenia also had a higher prevalence of elevated TAG content (>75 percentile) within the muscle compared to children without myopenia (36% vs 0%; p=0.009). Percent of muscle fibres with centralized nuclei were not different between groups. In conclusion, children with myopenia experience differences in skeletal muscle biological characteristics when compared to children without myopenia at LTx and these findings may have implications for dietary and exercise rehabilitation pre-and post-LTx.