Digital PCR (dPCR) and quantitative PCR (qPCR) methods were compared for their ability to detect mixed chimerism and predict relapse in leukemia patients after stem cell transplantation. Research results showed that dPCR using the QuantStudioTM 3D Digital PCR System produced similar results to qPCR when recipient DNA levels were above 1%, but was more sensitive for detecting lower levels of 0.2% or less. dPCR was able to detect increasing recipient chimerism earlier than qPCR in some samples, potentially allowing for earlier prediction of relapse. The false positive rate for dPCR was close to the 0.01% level considered full donor chimerism.