Background: 'Choke vessels' are thought to dilate in the first 72 h when blood flow to an area is disrupted. This study used 'high cut-off' microdialysis catheters in clinical research to investigate factors mediating circulatory change within free flaps. Methods: Six patients undergoing DIEP flap breast reconstruction each had three 'high cut-off' microdialysis catheters, with a membrane modification allowing molecules as large as 100 kDa to pass, inserted into Hartrampf zones 1, 2 and 4 to assess multiple vascular territories. Microdialysis continued for 72 h post-operatively. Samples were analysed for interleukin-6 (IL-6), tumour necrosis factor alpha (TNFα) and fibroblast growth factor basic (FGFβ). Results: Three hundred and twenty-four samples were analysed for IL-6, FGFβ and TNFα totalling 915 analyses. IL-6 showed an increasing trend until 36 h post-operatively before remaining relatively constant. Overall, there was an increase (p < 0.001) over the time period from 4 to 72 h, fitting a linear trend. TNFα had a peak around 20–24 h before a gradual decrease. There was a significant linear time trend (p = 0.029) between 4 and 76 h, decreasing over the time period. FGFβ concentrations did not appear to have any overall difference in concentration with time. The concentration however appeared to oscillate about a horizontal trend line. There were no differences between the DIEP zones in concentrations of cytokines collected. Conclusion: This study uses high-cut off microdialysis catheters to evaluate changes in cytokines, and requires further research to be undertaken to add to our knowledge of choke vessels and flap physiology. Level of evidence: Level IV, diagnostic study. [ABSTRACT FROM AUTHOR]