In this study, 13 different eluent systems containing n-hexane, n-heptane and iso-octane as main solvents and ACN, propionitrile (PCN) and butyronitrile (BCN) in concentrations between 0.1 and 0.2% as modifiers were tested for their influence on retention time shifts (RTS) and resolution of conjugated linoleic acid (CLA) methyl esters using two ChromSpher 5 Lipids columns (250 mm x 4.6 mm, 5 microm) in series. The eluent system n-hexane/PCN 0.2% showed the highest stability with an obtained RTS of 0.26 min for the cis/trans-group after 14 consecutive injections of a CLA isomer mix compared to the reference system of n-hexane/ACN 0.15% (RTS of 2.35 min). This enhanced stability is due to better solubility of PCN in n-hexane compared to ACN. The enhanced stability coincided with a negligible loss in resolution for the cis,trans/trans,cis- and the cis,cis-groups. As shown for the analysis of human aortic endothelial cells spiked with t10c12-CLA, data from CLA-analysis by Ag+-HPLC-DAD must be judged very carefully, especially at low concentrations, as coeluting matrix compounds may give false-positive results. Therefore, results should be confirmed by GC-FID and GC-MS.