Fatty acids profiles of Emiliania huxleyi strain CCMP1516 were determined in a virus-induced culture crash with E. huxleyi virus 86 (EhV-86). As cell numbers declined in the infected cultures due to virus lysis, a concomitant decrease in fatty acids was observed in the particulate fraction. The composition of fatty acids within infected E. huxleyi cells was restructured, with a shift from polyunsaturated to monounsaturated and saturated fatty acids (respective distributions changing from 70:10:20% at the start of the experiment to 44:24:32% at the final time point). In particular, decreases were seen in the major fatty acid 22:6(n-3) and in 18:5(n-3), whereas greatest increases were seen in 18:1(n-9) and 22:0. The increase in the amount and restructuring of the fatty acid pool in E. huxleyi was indicative of a combination of specific and non-specific effects of virus infection. Specific effects primarily included induction of metabolic pathways such as the synthesis of components involved in virus replication, the production of virions and signal transduction via sphingolipid biosynthesis. Non-specific effects due to stress were likely mediated by reactive oxygen species. Changes in the composition of virus-infected E. huxleyi are of significance to the food web since grazing on virus-infected blooms will decrease the amount of essential polyunsaturated fatty acids passed on to higher trophic levels. Consequently, this could decrease the overall productivity of marine ecosystems.