Viral–host interactions represent potential drug targets for novel antiviral strategies (Flisiak et al., Hepatology, 2008, 47, 817–26). Hence, it is important to establish an adequate platform for identifying and analyzing such interactions. In this review, we discuss bottlenecks in conventional protein–protein interaction methodologies and present the contribution of innovative microfluidic-based technologies towards a solution to these problems with respect to viral–host proteomics.