This article presents a cost-effectiveness study comparing cytogenetic and molecular analyses for detection of chromosomal abnormalities which are prognostic factors in acute leukemia. The aim of the study was to determine how these two techniques could substitute or complement one another. The study sample consisted of 107 adult patients with de novo myeloid or lymphoid acute leukemias, tested by both techniques in 1994 and 1995, for identification of translocations t(9;22), t(8;21), t(15;17), t(4;11), t(1;19), the inversion of chromosome 16 and for monosomy 5 or 7 (or deletion of their long arms) and trisomy 8. The criterion for diagnostic effectiveness of these strategies was the rate of detection of true positive anomalies which are clinically relevant, according to the current state of knowledge. On the basis of these observations six alternative strategies at diagnosis were compared (each technique alone or different combinations of the two techniques). The study shows that:-for ALL, PCR alone appears the most cost-effective strategy;-for AML, cytogenetic analysis alone is the best strategy;-sequential strategies are more cost effective than simultaneous use of both techniques for minimising risk of false negatives.