In recent years, there have been many Multiple Sclerosis (MS) studies using longitudinal MR images to study and characterize the MS lesion patterns. The intensity of similar anatomical tissues in MR images is often different because of the variability of the acquisition process and different scanners. This paper proposes a novel methodol-ogy for a longitudinal lesion analysis based on intensity standardization to minimize the inter-scan intensity difference. The intensity normaliza-tion maps parameters obtained using a robust Gaussian Mixture Model (GMM) estimation not affected by the presence of MS lesions. Experi-mental results demonstrate that our technique accurately performs the task of intensity standardization. We show consequently how the same technique can improve the results of longitudinal MS lesion detection.