In 2002, the Nobel Prize for chemistry was awarded to the inventors of two novel ionization techniques in mass spectrometry, MALDI and ESI. These techniques, often in combination with data from genomic databases, represent an extremely powerful tool in analytical (bio)chemistry, with many applications, e.g., in the field of proteomics. Peptides, which are small proteins, have, despite their importance as controlling agents in numerous physiological processes, as yet been much less intensively studied by these novel techniques than larger proteins. The term peptidomics, i.e., the study of all peptides expressed by a certain cell, organ or organism was only introduced in 2001. In neuroendocrinology, spectacular progress could already be realized and the future looks bright. In this minireview we discuss the different methodologies that are used in peptidomics and give an overview of the wide range of applications.