X-ray crystallography is the workhorse of large-scale structural biology initiatives that seek to understand protein function and interaction at the atomic scale. Despite impressive technological advances in X-ray sources, phasing techniques, and computing power, the determination of protein structure has been severely hampered by the difficulties in obtaining high-quality protein crystals. Emergent technologies utilizing microfluidics now have the potential to solve these problems on several levels, both by allowing researchers to conduct efficient assays in nanoliter reaction volumes, and by exploiting the properties of mass-transport at the micron scale to improve the crystallization process. Using the technique of Multilayer Soft Lithography (MSL) we have developed a set of microfluidic tools suitable for all stages of protein crystallogenesis, including protein solubility phase space mapping, crystallization screening, harvesting, and in situ diffraction studies. These tools represent the state of the art in on-chip fluid handling and have been demonstrated to dramatically improve protein crystallization. Beyond crystallization, the high levels of parallelization and programmable fluid handling functionality enable a broad range of applications in proteomics, biology and medicine.