BACKGROUND A single bout of strenuous running exercise results in perturbations to numerous biomarkers. An understanding of these is important when analysing samples from individuals who have recently performed such exercise. METHODS A literature search was undertaken using the search terms, exercise, marathon and delayed onset of muscle soreness. The search was then refined using the terms for key biomarkers known to be altered by exercise. RESULTS The magnitude of changes to biomarkers is proportional to the severity of the running bout. Familiar, moderate intensity running exercise produces brief transient changes in common biomarkers such as lactate, whereas more severe bouts of running exercise, such as marathons and ultra-marathon events can produce changes to biomarkers that are normally associated with pathology of the muscles, liver and heart. Examples being changes to concentrations and/or activity of myoglobin, leucocytes, creatine kinase, bilirubin, cardiac troponins, lactate dehydrogenase, alanine aminotransferase and aspartate aminotransferase. While persisting for longer, these changes are also transient and full recovery occurs within days, without any apparent long-term adverse consequences. Additionally, unfamiliar exercise involving forceful eccentric muscle contractions, such as running downhill, can cause increases in creatine kinase and delayed onset of muscle soreness that peaks 36-72 h after the exercise bout. CONCLUSIONS Strenuous running exercise can produce changes to biomarkers that are normally associated with disease and injury, but these do not necessarily reflect chronic pathology.