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The expression of the high mobility group protein gene HMGA2 is primarily confined to embryonic and fetal cells. The aim of this study was to determine the relative expression level of HMGA2 in cells of amniotic fluid samples. Furthermore, it should be investigated by chromatin immunoprecipitation whether or not HMGA2 is attached to cell-free DNA in amniotic fluid.Expression levels of HMGA2 in 58 amniotic fluid samples from the second trimester were measured using quantitative real-time polymerase chain reaction (PCR). Furthermore, the presence of HMGA2, attached to cell-free DNA was tested by chromatin immunoprecipitation.Expression of HMGA2 was detected in all samples, but in cells of the amniotic fluid it was 161-fold higher than in cells of the urine from healthy donors. The real-time PCR with GAPDH showed a signal in all samples treated with the improved protocol of immunoprecipitation.Our data clearly show that cells of the amniotic fluid strongly overexpress HMGA2 according to their fetal origin. The fact that apparently HMGA2 remains to be attached to cell-free DNA suggests interesting new approaches in noninvasive prenatal diagnosis.