How lymphocyte counts relate to treatment-response in patients with ANCA-associated vasculitis (AAV) is controversial, and data on short-term variability of lymphocyte counts are lacking. Retrospective single center evaluation of disease activity and lymphocyte counts in patients with AAV, and of lymphocyte counts in kidney transplant-recipients, were done; both at the University Hospital Basel, Switzerland. Twenty-three patients with AAV were included. Remission was achieved in all patients. Ten patients experienced a relapse after a median of 66 weeks (range 15-189 weeks). Median lymphocyte counts at diagnosis were significantly higher than at remission (1.38 x 10(9)/L vs. 0.99 x 10(9)/L; P = 0.007). By contrast, median lymphocyte counts at remission and relapse did not differ significantly. However, intra-individual variability of lymphocyte counts early after diagnosis was high [median lymphocyte variability-range during the first 3 weeks of treatment 1.57 (range 0.27-3.95), n = 17]. This variability was not specific to patients with AAV, but was also observed in patients after kidney transplantation [variability of 1.76 (range 0.74-3.95, n = 31)]. The significantly higher median lymphocyte counts at diagnosis of AAV make lymphocyte counts a valuable surrogate for the treatment-efficiency in clinical studies. By contrast, on a patient-level, variability of lymphocyte counts impedes meaningful interpretation of individual measurements.