In this thesis, acoustofluidics has been used to process blood samples as a sample preparation step prior to biomarker detection. This is often required as the large amount of blood cells otherwise can interfere with the detection method. Acoustofluidics means moving particles or cells with acoustic forces within microfluidic channels. Ultrasound is used to create a standing wave between the channel walls. By matching of the frequency to the channel with, a half wavelength standing wave can be created between the side walls. Blood cells introduced into this channel will then be focused to the centre pressure node while the plasma can be extracted from the sides. This approach has here been used for three different applications. First it was integrated with a prostate-specific antigen (PSA) immunoassay which not only enabled detection of PSA from whole blood but also resulted in a faster detection because of the continuous flow of produced plasma, constantly bringing new analyte close to the capturing antibodies. Secondly a similar blood plasma separation was integrated with an acoustic trap for enrichment and microchip PCR to enable fast identification of bacteria from sepsis blood samples. In a small clinical study this acoustofluidic based detection system could identify Escherichia coli (E. coli) in half of the samples compared to blood culture, probably the ones with the highest bacteria load. In an attempt to improve the bacteria recovery of the blood bacteria separation, another setup where buffer flow in the centre of the channel laminated the blood sample along the sides was tested. By carefully control the dilution of blood sample and the acoustic impedance (density times speed of sound) bacteria recovery was significantly improved. Third, simple and fast haematocrit (HCT) measurements were also achieved in an acoustofluidic device combined with image analysis. The area of the focused blood cells compared to the whole channel area gave a measure with linear relationship to HCT measure by standard methods. This way of measuring HCT could be used prior to the separation step in acoustofluidic sample preparation device. From this I conclude that acoustofluidic sample preparation, which continuously can produce plasma both from diluted and undiluted blood samples, is a promising tool for miniaturised, automated total analysis systems for the detection of rare biomarkers.