Hierlemann's research initially was mostly in the area of chemical sensors and microsensors. In particular, he worked on the detection of organic volatiles and the discrimination of enantiomers in the gas phase. He then adopted microtechnology and, specifically, CMOS-based microelectronics to devise complex microsensor systems. The current interdisciplinary research is rooted in engineering and physics and targeted at questions in biology and medicine. It includes the development of CMOS-based integrated chemical and biomicrosystems, as well as bioelectronics and high-density microelectrode arrays. The high-density microelectrode arrays are used for fundamental research in information processing and signaling characteristics of neurons or brain cells. Moreover, the research group is engaged in the development of microfluidics for investigating the characteristics of single cells and microtissues.
Applications of Hierlemanns and his groups technologies are in the fields of systems biology, drug testing, personalized medicine, and neuroscience.