In recent years, the role of zinc in biological systems has been a subject of intense research. Despite wide increase in our knowledge and understanding of zinc homeostasis, numerous questions remain to be answered, encouraging further research. In particular, the quantification of intracellular zinc ions and fluctuation, as well as the function of zinc in signaling processes are being intensely investigated. The determination of free intracellular zinc ions is difficult and error-prone, as concentrations are extremely low (in the pico- to nanomolar range), but techniques exist involving fluorescent probes and sensors. In spite of zinc deficiency being accepted as a global problem, causing death and disease worldwide, to date there are no markers to reliably assess a person’s zinc status. This review summarizes the difficulties and major pitfalls when working with zinc in in vitro and in vivo research. Additionally, it specifies important aspects for zinc substitution and supplementation, including the bioavailability of zinc and its intestinal absorption. In particular, it is intended to help researchers with yet minor experience working with zinc efficiently set up experiments and avoid commonly occurring mistakes, starting with the choice and preparation of reagents and instrumentation, and concluding with possibilities for measuring the status of zinc in humans.