Carotenoids are natural pigments synthesized by plants and photosynthetic microorganisms, some of which, like β-carotene, are precursors of vitamin A, and others such as lutein and lycopene might function in the prevention of age-related macular degeneration and prostate cancer, respectively. Mass spectrometry provides high sensitivity and selectivity for the identification and quantitative analysis of carotenoids in biological samples, and previous studies have described how atmospheric pressure chemical ionization (APCI) offers distinct advantages over electrospray and fast atom bombardment for the analysis of specific carotenoids. Since APCI product ion tandem mass spectra have been reported for only a few carotenoids, a detailed investigation of twelve carotenes and xanthophylls was carried out using both positive ion and negative ion APCI tandem mass spectrometry with collision-induced dissociation. Using protonated molecules as precursor ions in positive ion mode and radical anions in negative ion mode, characteristic fragment ions were identified that may be used to distinguish between carotenoids.