Background and purpose: To compare 3D-Fast Gray Matter Acquisition with Phase Sensitive Inversion Recovery (3D-FGAPSIR) with conventional 3D-Short-Tau Inversion Recovery (3D-STIR) and sagittal T1-and T2-weighted MRI dataset at 3 Tesla when detecting MS spinal cord lesions. Material and methods: This prospective single-center study was approved by an institutional review board and enrolled participants from December 2016 to August 2018. Two neuroradiologists blinded to all data, individually analyzed the 3D-FGAPSIR and the conventional datasets separately and in random order. Discrepancies were resolved by consensus by a third neuroradiologist. The primary judgment criterion was the number of MS spinal cord lesions. Secondary judgment criteria included lesion enhancement, lesion delineation, reader-reported confidence and lesion-to-cord-contrast-ratio. A Wilcoxon's test was used to compare the two datasets. Results: 51 participants were included. 3D-FGAPSIR detected significantly more lesions than the conventional dataset (344 versus 171 respectively, p<0.001). Two participants had no detected lesion on the conventional dataset, whereas 3D-FGAPSIR detected at least one lesion. 3/51 participants had a single enhancing lesion detected by both datasets. Lesion delineation and reader-reported confidence were significantly higher with 3D-FGAPSIR: 4.5 (IQR 1) versus 2 (IQR 0.5), p<0.0001 and 4.5 (IQR 1) versus 2.5 (IQR 0.5), p<0.0001. Lesion-to-cord-contrast-ratio was significantly higher using 3D-FGAPSIR as opposed to 3D-STIR and T2: 1.4 (IQR 0,3) versus 0.4 (IQR 0,1) and 0.3 (IQR 0,1)(p = 0.04). Correlations with clinical data and inter- and intra-observer agreements were higher with 3D-FGAPSIR. Conclusion: 3D-FGAPSIR improved overall MS spinal cord lesion detection as compared to conventional set and detected all enhancing lesions.