Introduction Peripheral neuropathy is highly prevalent in chronic kidney disease (CKD), occurring in 90–100% of patients receiving dialysis. Previous neurophysiological studies using nerve excitability techniques have demonstrated changes in axonal function following a single session of dialysis. The present study was undertaken to examine whether there were morphological changes that may accompany these alterations in nerve function. Methods 15 CKD patients on thrice-weekly high-flux haemodialysis were recruited and studies were conducted before and after a single session of haemodialysis. Serial measurements of median nerve cross-sectional area (CSA), echogenicity and intraneural blood flow were also performed at a non-entrapment site (distal forearm) using high resolution ultrasonography (10–18 MHz probe). Intraneural blood flow was measured by obtaining 5 twenty-second clips of Power Doppler sonograms. Intraneural blood flow and echogenicity data were semi-quantitatively analyzed using a specialized and well-validated software to obtain the median nerve perfusion intensity (PI) and the percentage of hypoechoic area (pHA) respectively. Corresponding nerve excitability studies were undertaken on median motor axons. Results Overall, there was a significant decrease in CSA and PI post-dialysis (p 0.05). A reduction in CSA occurred in 90% of patients (9.05 ± 0.89 mm2 vs 8.51 ± 0.98 mm2), while 80% and 75% had a decrease in PI (0.79 ± 0.47 cm/s vs 0.47 ± 0.24 cm/s) and pHA (56.0 ± 1.0% vs 55.0 ± 1.6) respectively. Furthermore, the change in morphological measures was significantly correlated with excitability indices of membrane potential (PI and depolarising threshold electrotonus r = 0.67 p 0.05). Conclusion This study demonstrates morphological changes in peripheral nerves following a single session of dialysis. These changes correlate with the extent of change in measures of axonal function and may contribute to the development of axonal injury in CKD.