We present our first experiences with determination of minimal residual disease (MRD) based on patient specific Flt3-ITD (internal tandem duplication) mutations. We analysed MRD status of 11 AML patients in a retrospective investigation and its potential impact on the follow up of these patients. In five out of six patients with a positive Flt3-ITD based MRD status a relapse of AML was observed in the follow up while one patient lacks a clinical relapse so far. In contrast, four out of five patients with a negative MRD status remain free of disease. One of these patients relapsed with a switch of FAB subtype including loss of Flt3-ITD mutation. Furthermore, in one patient we could identify a Flt3-ITT (internal tandem triplication mutation).