A method for automatic lineage assignment of acute leukemias. Eight four-parameter list mode data files are acquired with a flow cytometer in the following sequence: 1. unstained; 2. isotype controls; 3. CD10 FITC, CD19 PE; 4. CD20 FITC, CD5 PE; 5. CD3 FITC, CD22 PE; 6. CD7 FITC, CD33 PE; 7. HLADR FITC, CD13 PE and 8. CD34 FITC, CD38 PE. First, data files 3-8 are clustered employing an algorithm based on nearest neighbors. The clusters are then associated across the data files to form cell populations, using the assumption of light scatter invariance across tubes for each population. The mean positions of each cell population are compared to a decision tree which identifies normal cell populations. To identify leukemic cell populations, the algorithm eliminates normal cell populations from the data space and the remaining populations are classified as B-lineage ALL, T-lineage ALL, AML, AUL, B-CLL or unknown.