The development of high-throughput techniques, for example cDNA and oligonucleotide microarrays, for simultaneous analysis of the transcriptional expression of thousands of genes, even the entire genome, has provided new possibilities to get better insights into the pathogenesis of various diseases. This technology has also been applied to define biomarkers and, most importantly, possible new candidate targets for novel treatments. In multiple sclerosis, microarray studies have been performed on brain autopsy and biopsy specimens and peripheral blood. The effects of current treatments for multiple sclerosis, especially interferon-beta and glatiramer acetate, on transcriptional profiles, have also been investigated. We review the main findings revealed from these studies. The emerging potential of microarray technology to define gene signatures, diagnostic and prognostic markers for disease course, and treatment response in multiple sclerosis will be discussed.