Multiple Sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) and is characterized by inflammation, demyelination and desctruction of oligodendrocytes and axons. The immunology of MS is complex, involving autoreactive Th1 and Th17 lymphocytes, cells of the innate immune system including dedritic, natural killer (NK) and microglia cells, as well as vascular endothelial cells. Multiple Sclerosis (MS) is based by a series of biochemical changes affecting to different extent neuronal functions; great attention has been focused on: liver enzymes, thyroid function tests, autoantibodies, lipid profile and uric acid levels. Following the introduction of therapy with drugs that modify the course of disease, more attention has been paid to the change of biochemical parameters, in particular to evaluate possible adverse effects. Aim of this study was to perform a review of the literature on biochemical alterations in treated and untreated MS patients and to assess laboratory parameters alterations in a cohort of MS patients, before and during treatment. On a total of 624 patients followed at our center, we selected those who practiced for the first time a therapy with IFN beta 1a at various doses, IFN beta 1b and Glatiramer acetate, that were 595 (95%), with baseline biochemical evaluation available in 488 (82%) (307 females, mean age 36.6 years). We considered the evolution of various biochemical parameters during treatment. The following outcome variables were evaluated: laboratory changes, in particular liver function, thyroid function, lipids and blood cell count. Percentages were compared using the chisquare test. ANOVA was performed to evaluate changes of laboratory tests over time between therapy groups. Our finding confirm the presence of biochemical alterations at baseline, in particular regarding liver enzymes, thyroid hormones and lipids. Treatment effects were more evident on liver enzymes elevation, anti thyroid antibodies production and blood cholesterol decrease. These effects were mainly transient and self remitting without suspension of therapy. Biochemical alterations, mainly related to autoimmune pathology and lipid metabolism change were encountered. Treatments increased transient biochemical alterations particulary in patients with baseline changes, suggesting a stricter monitoring of blood exams in this category of patients.