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The diagnosis of aneuploidies via the detection of circulating fetal DNA from maternal circulation is impaired by low fetal fractions i.e. concentration of fetal DNA relatively to maternal DNA. Low fetal fractions (FF) result from poor sample management (sample collection procedures, delays in plasma extraction) or biological factors such as obesity. To alleviate sample rejection due to these factors we propose a microfluidic device capable of on-site enrichment of FF directly from maternal blood sample.This device simultaneously collects plasma and enriches FF from maternal DNA background via size-fractionation in an efficient single-step sample preparation process. Plasma from 8 male bearing patient blood samples was recovered from the microfluidic chips and centrifugation controls. Circulating DNA was purified for each sample series. qPCR amplification of male fetal DNA target DYS14 and a universal target, β-actin was used to quantify fetal DNA levels in the samples from patient bearing a male fetus.The microfluidic extraction resulted in a 3.5 fold average relative increase of FF relatively to the centrifugation control (p = 0.01, Student’s t-test). In plasma extracted through the microfluidic chip, the FF range was found to be 11.26–68.15% with a mean of 37.66% while centrifugation resulted in FF range of 0.06–25% with a mean of 10.73%.This device significantly enriches fetal DNA fractions from maternal blood without the need for expensive apparatus. It could be deployed near-patient to improve the recovery of fetal DNA, aneuploidy testing accuracy, and the ability to test NIPT samples with low fetal fractions.