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 70 +/- 75cm(2); for scans made with the same tube voltage this was 23 +/- 17cm(2). Agreement was excellent for both methods: ICC: 0952, SEM: 72cm(2), SDD95: 199cm(2) and ICC: 0997, SEM: 20cm(2), SDD95: 56cm(2), respectively. MRA of scans made with a different tube voltage differed 13 +/- 113 HU, and agreement was poor (ICC: 0207, SEM: 79 HU, SDD95: 218 HU). For scans made with the same tube voltage the difference was 67 +/- 32 HU, and agreement was good (ICC: 0682, SEM: 53 HU, SDD95: 146 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.