Strenuous, prolonged exercise increases interleukin-6 (IL-6) release. The effect of IL-6 is dependent on the availability of IL-6 receptors. Few studies have addressed the impact of exercise on IL-6 receptor levels or procalcitonin (PCT), an indicator of systemic inflammation. Changes in these molecules may give insight into cytokine-related mechanisms underlying exercise-related fatigue. Thirteen trained male subjects partook in the study. They cycled a total distance of 468 km over 6 days. Blood samples were obtained prior to and immediately following Day 1 of the study and then each morning prior to exercise. Blood samples were analysed for plasma IL-6, soluble IL-6 receptor (sIL-6R), C-reactive protein (CRP), PCT, creatine kinase (CK) and cortisol concentrations. Subjects also completed mood state questionnaires each day prior to exercise. IL-6 was elevated immediately post-exercise on Day 1 but was unchanged at rest for the duration of the event. In contrast, sIL-6R, CRP, PCT and CK concentrations were unchanged immediately post-exercise on Day 1 but were significantly elevated at rest over the duration of the event compared with pre-event baseline. sIL-6R was highly correlated to CRP. Cortisol concentrations remained unchanged at all time points. In conclusion, strenuous, prolonged exercise stimulated an acute phase response which was maintained throughout the 6-day event. sIL-6R increase is associated with CRP and may affect subjective sensations of post-exercise fatigue at rest.