Previous data suggest that perceived foot heat and comfort may not coincide with actual foot temperature during treadmill running and that different shoe and sock materials can variously impact foot temperature. The purpose of this experiment was to determine if there were significant differences in foot temperature produced by cotton versus synthetic socks during longer runs, which more closely resemble endurance training, and if subjects were able to perceive those differences in terms of either comfort or temperature. Twelve adult males (22.4 ± 1.8 yrs, 180.6 ± 1.2 cm, 70.1 ± 1.6 kg) participated on two separate occasions one week apart. Subjects ran for 30 minutes with two temperature probes attached to the lateral dorsal aspect of the right foot in the same location: one directly on the skin and the other on the sock. All subjects wore the same shoe model. Foot temperature, heart rate, heat perception, and comfort perception were recorded. Perception was measured by using 10 cm visual analogue scales. Each subject ran once in a cotton-based sock and once in a synthetic (olefin-based) sock. Subjects perceived no significant difference in comfort or temperature between cotton and synthetic socks, and heart rate did not vary significantly between the two trials. The olefin-based sock was associated with significantly lower absolute temperatures at the sock thermometer site but not the skin thermometer site. However, changes in temperature from one time point to the next were the same between the two socks for either thermometer site. The results cannot conclusively state that one sock has an advantage over the other, but they suggest olefin-based socks may dissipate heat better than cotton-based socks under certain conditions.