The biological mechanisms responsible for the association of specific karyotypes with prognosis in acute myeloid leukaemia (AML) remain largely unclear. A prospective study was performed to evaluate how far cytogenetically defined prognostic subgroups of AML differ in their proliferative activity as a potential mechanism for differential sensitivities to S‐phase‐specific induction chemotherapy comprising cytosine arabinoside (AraC). One hundred and eighty‐seven patients with de novo AML were included in the study; 25 patients with a favourable inv(16), t(8;21), t(15;17) karyotype, 99 with a normal karyotype, 29 with an unfavourable karyotype (−5, 5q–, −7, 7q–, complex aberrations) and 34 with cytogenetic aberrations of unknown prognostic significance (all others). The favourable group demonstrated the highest ex vivo proliferative activity (PA) (3·41 pmol/105 cells), significantly (P = 0·02) exceeding the unfavourable group with the lowest PA (0·72) and the group with a normal karyotype (1·06) or with karyotype of unknown significance (1·05) that both demonstrated an intermediate PA. Samples with a high PA (> median of the whole group) were more likely to produce interleukin 3, granulocyte macrophage colony‐stimulating factor (GM‐CSF), granulocyte CSF (G‐CSF) (56%, 43% and 50%) than cells with a low PA (33%, 36% and 36%; n.s.). The effect of priming by exogenous GM‐CSF or G‐CSF was significantly more pronounced in samples with a low PA than in rapidly proliferating samples (P < 0·01). For the whole group, a high PA was closely associated with an increased incorporation of AraC triphosphate (AraCTP) into the DNA (P < 0·0001). Clinically, a high PA was associated with a better complete remission (CR) rate in the normal (95% versus 62%) and the unfavourable group (75% versus 33%). The significant differences in proliferative activity between cytogenetic subgroups of AML are associated with increased cytosine arabinoside pharmacodynamics and constitute one potential mechanism for the different response of cytogenetic subgroups to AraC‐based induction therapy.