An efficient direct method for measuring c9,t11- and t10,c12-conjugated linoleic acid (CLA) isomer content in human and rat milk was developed and validated using an RTX-2330 capillary column (40 m x 0.18 mm x 0.1 microm). In comparison with the commonly used 100 m x 0.25 mm x 0.20 microm columns, this new type of fast column allowed the separation of FAMEs with the same resolution but in much less time. An additional advantage for biological samples was that only a small volume of sample was needed. Two different procedures were tested in order to select the best methylation of CLA isomers, and the alkali plus acid-catalyzed procedure was selected. The precision results showed relative standard deviations (R.S.D.) of repeatability and reproducibility ranging between 0.10 and 8.71%. The application of this method to human and rat milk samples showed that it was a rapid, simple and reliable method for the analysis of biological samples.