In peripheral arterial disease, patency, limb salvage, and survival rates are mostly reported using Kaplan-Meier analyses. When comparing different revascularisation techniques, these methods have limitations in analysing complex patient flows over time. This study aimed to present, illustrate, and discuss new concepts based on multistate models of analysing outcome parameters in peripheral arterial disease. Previously published data from a single centre, randomised controlled trial (RCT) with 218 cases that underwent either vein bypass surgery (bypass group, n = 109) or nitinol stent angioplasty (stent group, n = 109) of long femoropopliteal lesions were re-analysed using non-homogeneous Markov models. A step by step description of the concepts of states, state space, definitions, and illustration of transition probability curves as well as the benefits of multistate models is given. The RCT was registered at ISRCTN.com (ISRCTN18315574). Transition probability curves over time showed similar patterns in the bypass and stent groups. Significant differences in the transition probabilities were found for transitions from primary patency as well as secondary patency to end of patency. The transition probability for patients with preserved primary patency at 24 months who moved to end of patency at 48 months was 19.9% in the stent group vs. 6.4% in the bypass group (p < .001). The proposed method can answer important questions, such as: Did patients after femoropopliteal stenting with preserved primary patency at two years lose their patency more quickly within the following years compared with bypass surgery? and Did stent patients after a re-intervention to maintain patency at one year lose their patency more quickly compared with bypass surgery within the following years? Completely new research questions can now be raised and answered to optimise treatment and follow up strategies; this might lead to better identification of subgroups at higher risk of clinical deterioration following revascularisation procedures.