Conjugated linoleic acid (CLA) is produced by photoisomerization of soy oil linoleic acid. Yields increase with the degree of oil refining, but the effect of specific minor oil components is not known. Therefore, the objectives were to determine the effect of each soy oil minor component on CLA yields and oxidative stability after processing, to determine the effect of soy oil minor constituent interactions on CLA yields and oxidative stability, and to determine how soy oil Magnesol adsorption pretreatment affects CLA yields. Soy oils with varying levels of peroxides, tocopherols, phospholipids, free fatty acids (FFA), and lutein were each UV irradiated, and the CLA content and oxidative stability were determined. A peroxide value of above 0.8 greatly decreased CLA yields, as did phospholipids above 500 ppm. Tocopherols enhanced CLA production at low levels and reduced yields at high concentrations, while lutein and FFA had little effect. High CLA yields corresponded with a lower oil oxidative stability. The interactions between the minor components showed similar trends as seen in the single component study. These findings were supported by observations that Magnesol adsorption removed large quantities of phospholipids and peroxides from soy oil and greatly increased CLA yields but reduced the oxidative stability. Minor components, particularly peroxides and phospholipids, need to be removed from the oil to optimize CLA yields.