One of the most important parameters in Fluid-Attenuated Inversion Recovery (FLAIR) sequences MRI (FLAIR-MRI) is Echo Time (TE), so in this study we compare 100 ms and 165 ms echo time to diagnosis of Multiple Sclerosis (MS) lesions and use it for Flair-MRI protocol in MS patients. In this study we acquired FlAIR images at TE1=100 ms and TE2=165 ms with 1.5 Tesla (T) from 55 patients with MS. And then these images were studied to determine the number and location of MS lesions. Supratentorially and infratentorially, there were significant differences between the two sequences, in 100 ms echo time the number of lesions were 25.52 ± 20.69 (supratentorial), 0.58 ± 0.80 (infratentorial) and in 165 ms echo time 29.04 ± 20.69 (supratentorial), 0.67 ± 0.81 (infratentorial). (P Value=0.000). The presented results suggest that by increasing echo time of FlAIR-MRI diagnosis of MS lesions will be increased. So we can detect the lesions in early stages of the disease and also in follow-up studies.