Amyotrophic lateral sclerosis (ALS) is a devastating neurological disorder affecting upper and lower motoneurons. Since immune disbalance is known to be an important manifestation of the disease, working with the familial ALS rat model, hSODG93A (containing multiple copies of the human SOD1 G93A mutation), we were particularly interested in following by live magnetic resonance imaging (MRI) the immune cells labeled by ultra small paramagnetic iron oxide (USPIO) nanoparticles. In addition, microglial activation was studied by immunocytochemistry. MRI of USPIO labeled Tcells revealed CD4+ lymphocyte infiltration in the midbraininterbrain region while the CD8+ cells were more confined to the brainstem region. By way of gadolinium (Gd) contrast it was also confirmed that the bloodbrain barrier (BBB) was compromised. Moreover, it was revealed that the regions of BBB breakthrough were congruent with the MRI foci of Tcell infiltration. Immunocytochemistry revealed microglial activation and fusion, possibly phagocytic interactions with neurons in the hippocampus and brainstem. These observations prove the existence of an elaborate inflammatory process in the brain of hSODG93A rats, and also demonstrates the complexity and multifocality of ALS as having its inflammatory manifestations also in the central nervous system (hippocampus) distinct from clinically described motor foci of degeneration.