The incorporation pattern of conjugated linoleic acids (CLA) isomers into the egg yolk of hens in relation to that in the diet was studied. Silver-ion high-performance liquid chromatography (Ag-HPLC) was used to separate individual CLA isomers. It was found that the isomeric distribution pattern in the egg yolk lipids was different from that in the dietary fat. Total cis/trans isomers accounted for 81.2% of total CLA incorporated into the egg yolk, which was in contrast to the value of 92.0% of total CLA in the diet. Total cis/cis isomers accounted for 3.8% total CLA in the diet but they were 6.6% of the total CLA in the egg yolk lipids. In contrast, total trans/trans isomers were 12.2% of the total CLA isomers in the egg yolk lipids, whereas they were only 4.2% of total CLA in the diet. The results showed that total trans/trans-CLA was preferentially incorporated into the egg yolk, whereas the incorporation of total cis/trans-CLA isomers was partially discriminated. Within each group, the incorporation of individual isomers into the egg yolk lipids was also selective. cis-9,trans-11/trans-9,cis-11 and cis-10,trans-12/trans-10,cis-12 were the two major isomers in the diet. Ag-HPLC analysis showed that the former was preferentially transferred into the egg yolk compared with the latter. It was observed that supplementation of CLA in the diet of laying hens decreased the concentration of oleic acid (18:1n-9), arachidonic acid (20:4n-6), and docosahexaenoic acid (22:6n-3) but increased that of linolenic acid (18:3n-3), stearic acid (18:0), and palmitic acid (16:0) in the egg yolk, suggesting that CLA may inhibit Delta6 and Delta9 desaturases.