Understanding protein function and interaction is central to the elucidation of biological processes. Systematic analysis of protein interactions have shown that the eukaryotic proteome is highly interconnected and that biological function frequently depends on the orchestrated action of many proteins. Perturbation of these functions or interactions can lead to various disease states and pharmacologic intervention can result in corrective therapies. The fact that proteins rarely act in isolation, but rather comprise complex machines that stably and/or transiently interact with many different partners at different times, demands the need for robust tools that allow comprehensive global analyses of these events. Here we describe a powerful protein fusion technology, the HaloTag platform, and how it enables the study of many facets of protein biology by offering a broad choice of applications. We review the development of the key aspects of the technology and it’s performance in both in vitro and in vivo applications. In particular, we focus on HaloTag’s multifunctional utility in protein imaging, protein isolation and display, and in the study of protein complexes and interactions. We demonstrate it’s potential to help elucidate important facets of proteomic biology across complex biological systems at the biochemical, cell-based and whole animal level.