A computer program has been developed for computer-assisted diagnosis (including subclassification) of flow cytometry data of acute leukaemias and non-Hodgkin lymphomas by means of artificial intelligence. The knowledge base for the system has been formulated as semantic networks that describe physiological hematopoiesis as well as the pathological situation (e.g., aberrant antigen expression) of hematological disorders. The semantic networks reflect the hierarchy of cells and their occurrence in diseases, the normal and pathological antigen expression patterns of cells, cell maturation, and the frequency of cell populations in normal blood and bone marrow. Using these semantic networks, the diagnosis algorithm compares the characteristic antigen expression pattern of a disease with the actual findings in the blood or bone marrow sample. The algorithm can separate mixed populations by taking double staining findings into account. Finally, a diagnosis text is generated that describes all identified cell populations and the resulting diagnosis. The validation of the program showed a correct diagnosis (disease group and subclassification) in 97% of the cases (n = 633) with slight differences between the disease groups (e.g., B-NHL: 99%, B-cell ALL: 84%).