Internal tandem duplications (ITDs) of the FLT3 gene occur in approximately 20-30% of acute myeloid leukemia (AML) patients. We investigated if FLT3 ITDs could be used as minimal residual disease (MRD) markers for AML patients. Patient-specific polymerase chain reaction (PCR) assays for FLT3 ITDs were developed for four AML samples that contained FLT3 ITDs of varying size and location. The real-time, quantitative PCR assays for FLT3 ITDs were highly sensitive and specific, detecting between 0.01 and 0.001% of FLT3 ITD positive DNA in a background of 1 microg of normal bone marrow DNA. Our findings suggest that FLT3 ITDs can be used as molecular markers for MRD in patients with AML.