Flow limitations in the iliac arteries of endurance athletes during exercise were previously ascribed solely to intravascular lesions. We postulate that functional kinking of the arteries can also result in flow limitations. However, the diagnostic tools in routine practice are not effective in diagnosing such flow limitations in a substantial proportion of athletes, mainly because these diagnostic tools do not measure in the provocative situations. Ninety-two symptomatic legs in 80 endurance athletes were examined with newly developed, sports-specific vascular tests. Thirty-five asymptomatic cyclists matched for working capacity served as the control subjects. Legs were classified as vascular or non-vascular following a decision algorithm, based upon the results of these diagnostic tests, excluding orthopaedic causes by the effects of specific treatment. Independently of this clinical classification, an alternative method was applied to find stable characteristics in the total patient group using factor analysis. This characterisation was based on scores on 14 test variables deriving from diagnostic tests that were not used in the decision algorithm, thus avoiding dependency between the clinical categorisation and the statistical categorisation. The hypothesis was that these characteristics were sufficiently sensitive to classify patients with vascular and non-vascular complaints. If so, these characteristics should correspond with the one derived from the decision algorithm. Following the decision algorithm, 58 legs (63 %) were classified as vascular, 29 (32 %) as non-vascular and 5 (5 %) as inconclusive. The latter were considered non-vascular. In a substantial proportion of the vascular patients, kinking of the iliac arteries was identified as the major cause of flow limitation. The characteristics derived from factor analysis proved to classify 87 % in agreement with the decision algorithm (kappa 0.56). The agreement is sufficient for validation of the clinical classification. The algorithm can therefore be applied in clinical situations to diagnose endurance athletes with flow limitations due to both intravascular lesions and kinking of the arteries.