Kinetics of the formation of trans linoleic acid and trans linolenic acid were compared. Pilot plant-scale tests on canola oils were carried out to validate the laboratory-scale kinetic model of geometrical isomerization of polyunsaturated fatty acids described in our earlier publication. The reliability of the model was confirmed by statistical calculations. Formation of the individual trans linoleic and linolenic acids was studied, as well as the effect of the degree of isomerization on the distribution of the trans fatty acid isomers. Oil samples were deodorized at temperatures from 204 to 230°C from 2 to 86 h. Results showed an increase in the relative percentage of isomerized linolenic and linoleic acid with an increase in either the deodorization time or the temperature. The percentage of trans linoleic acid (compared to the total) after deodorization ranged from <1 to nearly 6%, whereas the percentage of trans linolenic acid ranged from <1 to >65%. Applying this model, the researchers determined the conditions required to produce a specially isomerized oil for a nutritional study. The practical applications of these trials are as follows: (i) the trans fatty acid level of refined oils can be predicted for given deodorization conditions, (ii) the conditions to meet increasingly strict consumer demands concerning the trans isomer content can be calculated, and (iii) the deodorizer design can be characterized by the deviation from the theoretical trans fatty acid content of the deodorized oil.