The aim of this study is to investigate if the three-dimensional (3D) double inversion recovery (DIR) sequence is superior compared to the 3D fluid-attenuated inversion-recovery (FLAIR) sequence in detecting intracortical, mixed, juxtacortical (JX), and deep grey matter (GM) lesions in multiple sclerosis (MS) patients. The correlation between intracortical lesion load and disability status was also investigated. Magnetic resonance imaging examinations of 24 patients (9 males, 15 females; mean age 34.4 +/- 12.0 (16-69) were retrospectively evaluated from our database. Lesions were counted and classified according to anatomic regions as intracortical, mixed, JX, and deep GM on the 3D DIR and FLAIR sequences. The incidence of lesions on the two sequences were identified and compared. The relationship between the number of lesions and type of MS, patient age, gender, duration of the disease, disability, the mean number of attacks per year and Expanded Disability Status Scale (EDSS) score was also investigated. More lesions were detected by the DIR sequence compared to the FLAIR sequence in all regions except for thalamus (11/12). The lesion detection superiority of DIR was statistically significant for intracortical lesions (p<0.001) and GM lesions (intracortical + mixed) (p<0.001). Lesion load of the JX area in the DIR sequence decreased as the disease duration (r=-0.444; p=0.030) and age (r=-0.473; p=0.020) increased. JX lesion load in the DIR sequence decreased as the number of attacks increased (r=-0.602; p=0.002). More mixed lesion load on the DIR sequence were found in cerebral atrophy group than in no cerebral atrophy group (p=0.026). EDSS score increased as the disease duration and number of attacks increased (p=0.003, p<0.001). There was no correlation between lesion location and EDSS score. The DIR sequence is superior to the FLAIR sequence in the detection of intracortical and GM lesions. Also, the mixed lesion load on the DIR sequence is correlated with cerebral atrophy.