A gas chromatographic procedure was used for the analysis of conjugated linoleic acid (CLA) isomers, c9t11-CLA and t10c12-CLA, in yoghurts containing Lactobacillus acidophilus or Bifidobacterium animalis and/or 2% fructooligosaccharide (FOS). Two groups of set yoghurts containing no supplement or 2% FOS were manufactured using three different starter cultures to determine the effect of processing, starter culture type, FOS supplementation and storage on CLA content. Processing of milk into yoghurt, the addition of FOS alone and storage for 28 d did not significantly affect CLA isomer formation in yoghurts (P > 0.05). However, significant increases in both isomer formation were obtained by using L. acidophilus or B. animalis in yoghurt manufacture (P < 0.05). The highest increases in c9t11-CLA isomer and total CLA content were found in yoghurts manufactured with L. acidophilus and FOS (2.71-fold increase in total CLA), and B. animalis and FOS (2.90-fold increase in total CLA) (P < 0.05). (c) 2007 Elsevier Ltd. All rights reserved.