Neurodegeneration is a very important process in the pathology of multiple sclerosis (MS). However, mechanisms leading to neurodegeneration in MS are still poorly understood. One of the most probable mechanisms triggering damage of the neuron is apoptosis induced by calcium-dependent enzymes. This review presents the mechanism of calcium overload of neuronal cell and also describes the direct and indirect mechanisms of neurodegeneration. Direct mechanism of neurodegeneration is induced by infiltration of the central nervous system (CNS) by immune cells like T-cells and macrophages and their direct damaging interactions with neurons. Many particular molecules like TRAIL, CD95, TNF-α, TNF-β on immune cells, and CD95/Fas/Apo-1, TNFR1, TNFR2, DR3/Wd1-1/Tramp, DR4/TRAIL-R1, DR5/TRAIL-R2/TRICK/Killer and DR6 on the CNS cells are involved in this process. The direct mechanism of neurodegeneration may be also induced by ROS (reactive oxygen species) and NO (nitric oxide) produced by macrophages and microglia in inflammatory foci. Indirect, secondary mechanism of neurodegeneration is mainly induced by primary demyelination. Furthermore, this paper describes in details the current knowledge about the possible markers of neurodegeneration in MS like neurofilaments; anti-neurofilaments antibodies; tubulin, actin and anti-tubulin, anti-actin antibodies; tau i fosfo-tau proteins; 24S-hydroxycholesterol (24S-ChOH); apolipoprotein E (ApoE); amyloid precursor protein (APP); N-acetylaspartate (NAA); 14-3-3 protein; neuron-specific enolase (NSE); and S100B (S100 calcium binding protein B).