Between 1986 and 2001, 220 patients with polycythaemia vera (PV) were studied using conventional cytogenetics. Of 204 evaluable patients, 52 (25·4%) had clonal abnormalities. The recurrent chromosomal rearrangements were those of chromosome 9 (21·1%), del(20q) (19·2%), trisomy 8 (19·2%), rearrangements of 13q (13·4%), abnormalities of 1q (11·5%), and of chromosomes 5 and 7 (9·6%). Subsequent analysis of 32 patients, performed at follow‐up of up to 14·8 years, revealed new clonal abnormalities in five patients and the disappearance of an abnormal clone in four. Eleven patients remained normal up to 11·5 years and seven patients maintained an abnormality for over 10 years. Fifty‐three patients were studied retrospectively using interphase fluorescence in situ hybridization (I‐FISH), utilizing probes for centromere enumeration of chromosomes 8 and 9, and for 13q14 and 20q12 loci. Conventional cytogenetics demonstrated clonal chromosome abnormalities in 23% of these 53 patients. The addition of I‐FISH increased the detection of abnormalities to 29% and permitted clarification of chromosome 9 rearrangements in an additional 5·6% of patients. FISH uncovered rearrangements of chromosome 9 in 53% of patients with an abnormal FISH pattern, which represented the most frequent genomic alteration in this series.