The aims of this study were to determine and compare the sensitivity of T2 turbo spin-echo (T2 TSE) and fluid-attenuated inversion recovery (FLAIR) sequences at 3.0 T in the detection of inflammatory lesions in patients with clinically isolated syndromes suggestive of multiple sclerosis. Forty-nine patients were examined with a 3.0 T MRI system using 5 mm axial sections of T2 TSE (2:19 min), FLAIR (4:00 min) and pre- and postcontrast T1 spin-echo sequences (3:37 min). Brain lesions were counted and categorized according to their anatomic location. Patients were classified according to Barkhof MRI criteria for FLAIR and T2 TSE sequences. The FLAIR sequence detected more lesions in every anatomic region except for the infratentorial region. The higher sensitivity was significant for the total number of lesions (p<0.01), the juxtacortical (p<0.01), and the periventricular (p=0.01) region. A 9% increase of infratentorial lesions using the T2 TSE sequence was not significant. The higher sensitivity using the FLAIR sequence resulted in one additional MRI criterion in nine patients, whereas the better detection of infratentorial lesions using the T2 TSE sequence resulted in additional MRI criteria in three patients. In conclusion, FLAIR provides the highest sensitivity when compared with the T2 TSE, although T2 TSE still has a diagnostic relevance in terms of MRI criteria classification.