Cytogenetic findings at diagnosis have influence on prognosis in patients with acute myelogenous leukaemia (AML) or MDS who undergo induction chemotherapy. Assessment of remission and treatment decisions are based on cytological findings. We analyzed the prognostic impact of cytogenetic remission status in 118 patients with abnormal karyotype who received induction chemotherapy. Initial cytogenetics were: 28 good-risk (14x t(15;17), 9x t(8;21), 5x inv(16)), 44 intermediate-risk, and 46 high-risk karyotypes. Eighty-three patients achieved complete remission (CR) and 20 achieved partial remission. Twenty-six of the patients who reached cytological CR retained an abnormal karyotype after induction, 13 of whom had been classified as standard-risk and therefore did not receive intensified consolidation. Sixty-one patients achieved cytogenetic CR (CCR), including 24 out of 28 (86%) patients with low-risk cytogenetics. The CCR rate was lower in patients with intermediate-risk (48%) or poor-risk cytogenetics (28%). Median survival (excluding patients with AML M3) of the CCR group was 37 months, as compared to 11 months in patients with persistence of abnormal karyotype (p < 0.0001). This difference remained statistically significant when calculated only for patients with intermediate-risk karyotypes (p = 0.03). Cytogenetic analysis after induction chemotherapy provides meaningful information especially in patients with intermediate-risk karyotypes. Patients with a persisting abnormal karyotype must be regarded as high-risk patients who should receive intensified treatment.