The microbes that reside in our human body make up our microbiota, and their genes are known as the microbiome. The gut microbiota is involved in a wide variety of functions. At present there is considerable evidence indicating that in the last 60 years there has been an important change in the composition of our microbiota. Dietary changes have been shown to have important effects on the microbiota in a very short space of time. The Mediterranean diet pattern causes changes in the microbiota towards a healthier profile. The changes induced by the Mediterranean diet could be explained, to a large extent, by its richness in polyphenols.