A significant fraction of atmospheric aerosol particles is composed of organic material with a highly complex but poorly characterized composition. For a better understanding of aerosol effects and processes in the atmosphere, a more detailed knowledge of aerosol components at a molecular level is needed. Peroxy acids might play a significant role in particle toxicity, due to their oxidizing properties, and they were recently found to be involved in particle formation. Because of the lack of appropriate standards, the identification and quantification of peroxy acids is often highly uncertain. Mass spectrometry (MS) is a powerful tool to characterize unidentified compounds in complex mixtures. However, so far there is only little information regarding the ionization and fragmentation behavior of peroxy acids in mass spectrometers. To study their fragmentation patterns, we synthesized 12 peroxy acids with C8 to C10 carbon backbones and mono- or diperoxy acid functionality. The peroxy acids were separated using liquid chromatography, detected via negative mode electrospray ionization high-resolution MS, and their fragmentation patterns (MS/MS spectra) were identified. The MS/MS spectra of the peroxy acids showed fragmentation patterns clearly different from the corresponding acid, with a strong similarity between compounds of different chain length but analogous functional groups. Neutral loss of CH2O2 was observed for all investigated linear peroxy acids but not for carboxylic acids and could therefore serve as a diagnostic ion for peroxy acids. The obtained results are a large step toward unambiguous characterization of peroxy acids in the atmosphere.