In order to meet the growing demand for high fuel burnup in nuclear reactors, the performance limits of zirconium (Zr)–based alloys, particularly Zircaloy-4, have been the focus of continuous research and development. As the nature, size, and distribution of second phase(s) in Zr matrix significantly influence all principal in-reactor properties (mechanical performance, oxidation kinetics/hydrogen uptake, and amorphization behavior) of the alloy, a great deal of research has been dedicated to investigating the second phases therein. This article comprehensively reviews the crystallographic features of second phases in Zr alloys with special weightage given to traditional Zircaloy-4 and that which is modified with Si and Ge. The crystallographic features of major nonequilibrium allotropes of Zr, such as room temperature β, ω, and face-centered-cubic phases, are described. Then, a variety of intermetallic second phase particles are dealt with in order to elucidate their crystallography of precipitation, crystalline defect substructures, and fracture characteristics. This review aims at providing an insight into the crystallography of second phases so that their further manipulation during processing can be realized in order to optimize in-reactor performance of the alloy.