This study aimed to compare the within-patient variability in haemoglobin levels in haemodialysis patients receiving intravenous epoetin alfa or intravenous darbepoetin alfa. Data on haemodialysis patients were extracted from the Renal Anaemia Management database from 2003 to 2004. The variance in haemoglobin was calculated for each patient with more than five haemoglobin observations (n = 3619). A mixed model was fitted to the within-patient variances and weighting was based on the number of observations minus 1 for each patient. The model took into account the situation where patients had data on both agents and could therefore act as their own control. The mean within-patient variance in haemoglobin levels for patients receiving darbepoetin alfa was 24% (95% CI: 18%, 31%) greater than that for patients receiving epoetin alfa (P < 0.0001). The mean haemoglobin level for patients receiving darbepoetin alfa was 11.33 g/dL (95% CI: 11.27, 11.40) compared with 11.43 g/dL (95% CI: 11.39, 11.46) for patients receiving epoetin alfa (P < 0.01). There was greater within-patient fluctuation in haemoglobin levels in patients receiving darbepoetin alfa compared with epoetin alfa. The implications of haemoglobin fluctuations on patient outcomes and resource use require further study.