The electron ionization (EI) mass spectral fragmentation of the trimethylsilyl derivatives of 3-methylidene-7,11,15-trimethylhexadecane-1,2-diol, Z- and E-3,7,11,15-tetramethylhexadec-3-ene-1,2-diols and Z- and E-3,7,11,15-tetramethylhexadec-2-ene-1,4-diols resulting from chlorophyll phytyl side-chain photo- and autoxidation was investigated. Different pathways (substantiated by deuterium labelling) were proposed in order to explain the main fragmentation observed. Then, some sufficiently specific fragment ions were selected and used to characterize these compounds in natural environmental samples.