Low skeletal muscle area (SMA) and muscle radiation attenuation (MRA) have been associated with poor prognosis in various patient populations. Both non-contrast and contrast CT scans are used to determine SMA and MRA. The effect of the use of a contrast agent on SMA and MRA is unknown. Therefore, we investigated agreement between these two scan options. SMA and MRA of 41 healthy individuals were analysed on a paired non-contrast and contrast single CT scan, and agreement between paired scan results was assessed with use of Bland-Altman plots, intraclass correlation coefficients (ICCs), standard error of measurements (SEM) and smallest detectable differences at a 95% confidence level (SDD95). Analyses were stratified by tube voltage. Difference in SMA between non-contrast and contrast scans made with a different tube voltage was 7·0 ± 7·5 cm2; for scans made with the same tube voltage this was 2·3 ± 1·7 cm2. Agreement was excellent for both methods: ICC: 0·952, SEM: 7·2 cm2, SDD95: 19·9 cm2 and ICC: 0·997, SEM: 2·0 cm2, SDD95: 5·6 cm2, respectively. MRA of scans made with a different tube voltage differed 1·3 ± 11·3 HU, and agreement was poor (ICC: 0·207, SEM: 7·9 HU, SDD95: 21·8 HU). For scans made with the same tube voltage the difference was 6·7 ± 3·2 HU, and agreement was good (ICC: 0·682, SEM: 5·3 HU, SDD95: 14·6 HU). In conclusion, SMA and MRA can be slightly influenced by the use of contrast agent. To minimise measurement error, image acquisition parameters of the scans should be similar.