Abstract: The present invention provides methods and compositions useful for diagnosing and choosing treatment for leukemia patients. The claimed methods include methods of assigning a subject affected by leukemia to a leukemia risk group, methods of predicting whether a subject affected by leukemia has an increased risk of relapse, methods of predicting whether a subject affected by leukemia has an increased risk of developing secondary acute myeloid leukemia, methods to aid in the determination of a prognosis for a subject affected by leukemia, methods of choosing a therapy for a subject affected by leukemia, and methods of monitoring the disease state in a subject undergoing one or more therapies for leukemia. The claimed compositions include arrays having capture probes for the differentially-expressed genes of the invention, computer readable media having digitally-encoded expression profiles associated with leukemia risk groups, and kits for diagnosing and choosing therapy for leukemia patients.