The aim of the present study was to investigate the effects of dietary trans fatty acids in mice. Following the administration of a 0.5/100 g diet of trans-9 octadecenoic acid (EA), trans-11 vaccenic acid (TVA) or cis-9, trans-11 conjugated linoleic acid (CLA) for 4 weeks, the body weights and the weights of the liver, testis and mediastinal adipose tissue (MAT) of the animals gradually decreased (P<0.05). The EA group exhibited the lowest levels of magnesium and triglycerides (P<0.05). CLA increased villus length (P<0.05), while EA and TVA decreased villus length (P<0.05). The TVA group exhibited the lowest levels of low-density lipoprotein and tumor necrosis factor-α (P<0.05). Taken together, EA, TVA and CLA affected the physiological conditions of mice differently. The potential effects of three well-known fatty acids, including trans-9 octadecenoic acid (EA), trans-11 vaccenic acid (TVA) and cis-9, trans-11 conjugated linoleic acid (CLA), in animals or humans remain to be elucidated. Therefore, in the present study, 32 animals were randomly divided into four groups and administered a 0.5/100 g diet of EA, TVA or CLA for 4 weeks. The results demonstrated that the body weights and the weights of the liver, testis and mediastinal adipose tissue (MAT) of the animals gradually decreased (P<0.05). Blood was collected individually via the external jugular veins and the EA group exhibited the lowest levels of magnesium and triglycerides (P<0.05). CLA increased villus length (P<0.05), while EA and TVA decreased villus length (P<0.05). The TVA group exhibited the lowest levels of low-density lipoprotein and tumor necrosis factor-α (P<0.05). Taken together, EA, TVA and CLA affected the physiological conditions of mice differently and these may further our understanding of the various effects of these fatty acids on animals and humans.