Although viruses can significantly reduce primary production-mediated carbon cycling, the effect of viral infection on the principal photosynthetic pigment that enables autotrophic production, chlorophyll a (chl a), remains unresolved. We compared the production of chl a transformation compounds in Emiliania huxleyi cultures undergoing viral infection with that in control cultures left to decline in the stationary phase of growth. A high performance liquid chromatography mass spectrometry method developed for the detection of Type I chl a transformation products was used. A rapid decline in cellular concentrations of chl a, C-13(2) diastereomer of chl a (chl a') and phaeophytin a (phytin a) was observed in both infected and control cultures. The most notable finding was the significant increase in the cellular concentrations of Type I chl oxidation products (allomers) in the infected cultures, and we hypothesise that this may be due to increased oxidative stress and reactive oxygen species.