Functional polymer coatings have become ubiquitous in biological applications, ranging from biomaterials and drug delivery to manufacturing-scale separation of biomolecules using functional membranes. Recent advances in the technology of chemical vapor deposition (CVD) have enabled precise control of the polymer chemistry, coating thickness, and conformality. That comprehensive control of surface properties has been used to elicit desirable interactions at the interface between synthetic materials and living organisms, making vapor-deposited functional polymers uniquely suitable for biological applications. This review captures the recent technological development in vapor-deposited functional polymer coatings, highlighting their biological applications, including membrane-based bio-separations, biosensing and bio-MEMS, drug delivery, and tissue engineering. The conformal nature of vapor-deposited coatings ensures uniform coverage over micro- and nano-structured surfaces, allowing the independent optimization of surface and bulk properties. The substrate-independence of CVD techniques enables facile transfer of surface characteristics among different applications. The vapor-deposited functional polymer thin films tend to be biocompatible because they are free of remnant toxic solvents and precursor molecules, potentially lowering the barrier to clinical success.