We investigated the applicability of FTIR-spectroscopy as a high throughput screening method for detection of biochemical changes in intact liver cells in bulk upon fatty acid exposure. HepG2 cells adapted to serum free (HepG2-SF) growth were exposed to four different fatty acids, three octadecenoic acids, differing in cis/trans-configuration or double bond position (oleic acid, elaidic acid and vaccenic acid) as well as palmitic acid in three days. High throughput FTIR spectroscopic measurements on dried films of intact cells showed spectra with high signal-to-noise ratio and great reproducibility. When applying principal component analysis (PCA) a clear discrimination between fatty acid exposures was observed. Higher levels of triacylglycerides were accumulated in cells exposed to elaidic acid than when exposed to the other fatty acids; the least accumulation appeared to be in cells exposed to palmitic acid. An increased absorption at ~966 cm(-1) corresponding to trans-double bond was detected upon elaidic acid exposure but not upon vaccenic acid exposure. Instead, upon vaccenic acid exposure two new absorption bands were observed at 981 and 946 cm(-1) due to the presence of double bond conjugation. Raman spectroscopy on single cells, with and without treatment by vaccenic acid, confirmed the presence of conjugation. By fatty acid composition analysis, the conjugation was further specified to be conjugated linoleic acid (CLA) isomers. Thus, instead of being preserved as a monounsaturated fatty acid, vaccenic acid was converted into CLA in HepG2 cells. The results demonstrate the applicability of high-throughput FTIR spectroscopy as an explorative method in in vitro systems from which biologically relevant hypotheses can be generated and further investigated.