Peripheral arterial disease severity ranges from asymptomatic (Fontaine stage I) through intermittent claudication (Fontaine stage II) to critical ischaemia (stage III and IV). Supervised exercise training is the main therapy used for PAD in the intermittent claudication stage. The aim of this article is to review the current literature in order to highlight known factors of PAD pathophysiology that change significantly after long-term exercise training and to determine future predictors for the effectiveness of PAD claudicants rehabilitation treatment. PubMed were searched for articles published during the last 23 years. The focus was on prospective randomized studies with control group, with long-term exercise training models that have met the EBM criteria. Except for the combination of traditional, nonspecific atherosclerosis factors only: 1) nitric oxide metabolite plasma concentrations as a marker of endothelial cell function, 2) plasma fibrinolysis activity and 3) obtained from gastrocnemius muscle biopsy markers of angiogenesis and myosin heavy chain (MHC) protein change significantly before and after physical rehabilitation in PAD patients with intermittent claudication. There is limited data on the associations between atherosclerosis markers as predictors of exercise training effectiveness in peripheral atherosclerosis. The current review contributes to a better understanding of the mechanisms that lead to the improvement of the clinical status of patients with intermittent claudication in the course of long-term physical training. Clearly, there is a need for further studies to understand the biochemical mechanisms involved in vascular changes due to physical rehabilitation.