With expanding kidney transplantation programs, remaining hemodialysis patients are more likely to have a high comorbidity burden and may therefore be more prone to lose muscle mass. Our aim was to analyze risk factors for muscle loss in hemodialysis patients with high comorbidity. Fifty-four chronic hemodialysis patients (Charlson Comorbidity Index 9.0 ± 3.4) were followed for 20 weeks using 4-weekly measurements of lean tissue mass, intracellular water, and body cell mass (proxies for muscle mass), handgrip strength (HGS), and biochemical parameters. Mixed models were used to analyze covariate effects on LTM. LTM (−6.4 kg, interquartile range [IQR] −8.1 to −4.8), HGS (−1.9 kg, IQR −3.1 to −0.7), intracellular water (−2.11 L, IQR −2.9 to −1.4) and body cell mass (−4.30 kg, IQR −5.9 to −2.9) decreased in all patients. Conversely, adipose tissue mass increased (4.5 kg, IQR 2.7 to 6.2), resulting in no significant change in body weight (−0.5 kg, IQR −1.0 to 0.1). Independent risk factors for LTM loss over time were male sex (−0.26 kg/week, 95% CI −0.33 to −0.19), C-reactive protein above median (−0.1 kg/week, 95% CI −0.2 to −0.001), and baseline lean tissue index ³10th percentile (−1.6 kg/week, 95% CI −2.1 to −1.0). Age, dialysis vintage, serum albumin, comorbidity index, and diabetes did not significantly affect LTM loss over time. In this cohort with high comorbidity, we found universal and prominent muscle loss, which was further accelerated by male sex and inflammation. Stable body weight may mask muscle loss because of concurrent fat gain. Our data emphasize the need to assess body composition in all hemodialysis patients and call for studies to analyze whether intervention with nutrition or exercise may curtail muscle loss in the most vulnerable hemodialysis patients.