Hydroperoxides formed by autoxidation of common fragrance terpenes are strong allergens and known to cause allergic contact dermatitis (ACD), a common skin disease caused by low molecular weight chemicals. Until now, no suitable methods for chemical analyses of monoterpene hydroperoxides have been available. Their thermolability prohibits the use of gas chromatography and their low UV-absorption properties do not promote sensitive analytical methods by liquid chromatography based on UV detection. In our study, we have investigated different liquid chromatography/mass spectrometry (LC/MS) ionization techniques, electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), and atmospheric pressure photoionization (APPI), for detection of hydroperoxides from linalool and limonene.Flow injection analysis was used to evaluate the three different techniques to ionize the monoterpene hydroperoxides, linalool hydroperoxide and limonene hydroperoxide, by estimating the signal efficacy under experimental conditions for positive and negative ionization modes. The intensities for the species [M+H]+ and [M+H-H2O]+ in positive ionization mode and [M-H]- and [M-H-H2O]- in negative ionization mode were monitored. It was demonstrated that the mobile phase composition and instrumental parameters have major influences on the ionization efficiency of these compounds. ESI and APCI were both found to be appropriate as ionization techniques for detection of the two hydroperoxides. However, APPI was less suitable as ionization technique for the investigated hydroperoxides.