Vascular calcification describes the formation of mineralized tissue within the blood vessel wall, and it is highly associated with increased cardiovascular morbidity and mortality in patients with chronic kidney disease, diabetes and atherosclerosis. In this article, we briefly review different rodent models used to study vascular calcification in vivo, and critically assess the strengths and weaknesses of the current techniques used to analyze and quantify calcification in these models, namely 2-D histology and the o-cresolphthalein assay. In the light of this, we examine X-ray micro-computed tomography (µCT) as an emerging complementary tool for the analysis of vascular calcification in animal models. We demonstrate that this non-destructive technique allows us to simultaneously quantify and localize calcification in an intact vessel in 3-D, and we consider recent advances in µCT sample preparation techniques. We discuss combining 3-D µCT analyses and subsequent 2-D histological, immunohistochemical and proteomic approaches in correlative microscopy workflows, to obtain rich multifaceted information on calcification volume, calcification load and signaling mechanisms from within the same arterial segment. We conclude by briefly discussing the potential use of µCT to visualize and measure vascular calcification in vivo, which could enable vascular calcification to be analyzed in real time in the future.