Microfluidic systems have become an attractive platform for diagnostic applications. The technology not only allows drastically decreased assay volumes (down to picoliters), but also accelerates sample processing and readout. In this article we give an overview of the different kinds of systems, ranging from non- or minimally instrumented point-of-care devices for the detection of pathogens to fully-instrumented cutting-edge technologies such as next-generation sequencing and droplet-based microfluidics. We expect that microfluidic systems will have a major impact on future diagnostic (e.g., disposable devices) and therapeutic approaches (e.g., personalized medicine). Here we summarize current trends and critically review the limitations.