To gain more insight into the immunophenotypic and cytogenetic changes in acute leukaemia at relapse, 99 Korean patients treated at a single institution were studied: acute myelogenous leukaemia (AML, n=46), acute lymphoblastic leukaemia (ALL, n=44) and biphenotypic and mixed leukaemia (n=9). Immunophenotypic changes at relapse were observed in 51 of 99 patients (51.5%) with almost even distribution in AML and ALL. Overall expression of aberrant markers on leukaemic cells was more frequent at relapse than at initial diagnosis (P < 0.05), and this finding was most prominent in B lineage ALL (41.4% versus 10.3%, P=0.007). Gain of aberrant CD13 or CD33 at relapse of B lineage ALL was most frequently observed. Cytogenetic changes at relapse were observed in 28 of 46 patients (60.8%). The initially abnormal karyotypes were more frequently associated with clonal changes at relapse compared to initially normal karyotypes (78.3% versus 43.5%, P=0.016). Cytogenetic changes were more frequent in B lineage ALL than in AML (90% versus 47.8%, P=0.05). In ALL, patients showing cytogenetic changes at relapse were significantly younger than those showing no changes (mean age of 15.0 versus 38.8, P=0.002), whereas in AML there was no significant difference between the two groups. In conclusion, the gain of aberrant markers and cytogenetic changes at relapse, which are suggestive of clonal instability, are more prevalent in B lineage ALL compared to AML, and lymphoid leukaemic cells of younger patients are more susceptible to clonal changes at relapse.