The completion of the Human Genome Project, and the innovations introduced in biotechnology are changing how to study twins. Here, we summarize some molecular studies performed on populations of discordant monozygotic twins (MZ) applying microarrays. Microarrays are an orderly arrangement of high numbers of probes (DNA, RNA or proteins), immobilized onto a matrix. The microarray approach allows a global analysis of gene expression, and therefore might point out the molecular mechanisms of MZ twins' discordance, such as epigenetic mechanisms. The application of microarray to twin studies will help better define, through bioinformatics, the role of genes and environment in the development of human diseases, thus suggesting new diagnostic and therapeutic approaches.