A complete diagnostic procedure was developed to detect single molecules of the AML1-ETO mRNA in whole blood and bone marrow samples of leukemia t(8;21)(q22;q22) patients. The procedure includes a method of preservation of biological samples to ensure RNA integrity, an improved method of RNA isolation from whole blood and bone marrow, an optimized reverse transcription protocol, and the use of nanocolonies to detect and quantify the target RNA molecules. The procedure is the first to report the absolute titer of an RNA target without reference to a control (housekeeping) gene and significantly increases the sensitivity, accuracy, and reliability of detection of the minimal residual disease in leukemia associated with a known chromosomal translocation.