Infertility can be considered a complex phenotype in the same way as cancer, cardiovascular and neurodegenerative diseases. Discovering a contributing factor and characterizing its contribution to a complex disease is a difficult undertaking, because the effect of any single factor may be obscured or confounded by other contributing factors. Determining the molecular markers associated with the disease could be useful in identifying its pathogenic mechanisms and consequently possible therapeutic options. In recent years, it has become evident that noncoding RNAs may represent specific molecular markers of disease. In fact, alterations of their expression were found in the pathogenesis of human diseases and it is known that altered regulation of microRNA expression affects crucial pathways for follicle growth and oocyte maturation in reproductive diseases such as PCOS and endometriosis.In reproductive medicine the identification of molecular markers is not only an important requirement for understanding the molecular basis underlying human infertility, but it also opens the chance to design individualized intervention protocols and therapies.