Trans fatty acids (TFA) and n-3 polyunsaturated fatty acids (n-3 PUFA) have opposite effects on several biological functions. We report a study on the effects on risk markers for cardiovascular disease. Eighty-seven healthy males were randomly assigned to 8 weeks of daily intake of either 20 g of industrially produced TFA (IP-TFA), 4 g n-3 PUFA, or control fat, incorporated in bakery products as part of the daily food. High-density lipoprotein cholesterol decreased in the TFA-group, triglycerides and mean arterial blood pressure decreased in the n-3 group. Heart rate variability (HRV), arterial dilatory capacity, flow mediated vasodilation, compliance, and distensibility were unchanged. Post hoc, we did a subgroup analysis of the results from the subjects with normal initial HRV. In these, 24-h heart rate (HR) was significantly increased by approximately three beats/min in the TFA group, with a decrease of the same magnitude in the n-3 group. A high HR is associated to an increased mortality and vice versa. Our results thus support the notion that IP-TFA and n-3 PUFA affect risk for cardiovascular mortality via mechanisms not only related to changes in plasma concentrations of lipids and lipoproteins.