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To evaluate the effect of a skeletal muscle index derived from a routine CT image at the level of vertebral body L3 (L3SMI) on outcomes of extubated patients in the surgical intensive care unit.231 patients of a prospective observational trial (NCT01967056) who had undergone CT within 5 days of extubation were included. L3SMI was computed using semi-automated segmentation. Primary outcomes were pneumonia within 30 days of extubation, adverse discharge disposition and 30-day mortality. Secondary outcomes included re-intubation within 72 h, total hospital costs, ICU length of stay (LOS), post-extubation LOS and total hospital LOS. Outcomes were analyzed using multivariable regression models with a priori-defined covariates height, gender, age, APACHE II score and Charlson Comorbidity Index.L3SMI was an independent predictor of pneumonia (aOR 0.96; 95% CI 0.941–0.986; P = 0.002), adverse discharge disposition (aOR 0.98; 95% CI 0.957–0.999; P = 0.044) and 30-day mortality (aOR 0.94; 95% CI 0.890–0.995; P = 0.033). L3SMI was significantly lower in re-intubated patients (P = 0.024). Secondary analyses suggest that L3SMI is associated with total hospital costs (P = 0.043) and LOS post-extubation (P = 0.048).The lumbar skeletal muscle index, derived from routine abdominal CT, is an objective prognostic tool at the time of extubation.Lumbar skeletal muscle index is an objective prognostic tool in ICU patients.L3SMI independently predicts pneumonia, adverse discharge and 30-day mortality.L3SMI can be derived from a single axial CT image with minimal training.Simplified model including only L3SMI and age predicts primary outcomes.CT metrics add clinically useful prognostic information without additional cost.