Using observations from the VIMOS Ultra-Deep Survey (VUDS), a massive spectroscopic campaign targeting 10,000 typical star-forming galaxies at 2 < z < 6, in conjunction with other surveys we have uncovered a large number of proto-structures that appear to resemble clusters and groups forming in the early universe. Though ostensibly a field survey, a number of factors relating to the survey itself and intrinsic to proto-structures have allowed VUDS to sample a large range of local and global densities at these redshifts. In this talk, I will discuss the development of the methods for finding, confirming, and characterizing proto-clusters and proto-groups in the context of VUDS including new techniques and tools developed specifically for these purposes. Several case studies of spectroscopically confirmed massive proto-clusters will be presented, focused both on the diversity of their global properties and that of their member populations. I will also discuss preliminary work on the full ensemble of VUDS proto-structures as well as measurements of the star formation rate-density and color-density relations at these redshifts.