The use of fluorochromes in bone research is a widely accepted technique that dates back to the 1950s. Several pioneers, such as Harold Frost, have thoroughly investigated the potential of fluorochrome use for the study on bone formation and bone remodeling dynamics. Since the development of bone tissue engineering, a renewed interest in the benefits of fluorochrome use was perceived. Fluorochrome use in animal models makes it possible to determine the onset time and location of osteogenesis, which are the fundamental parameters in bone tissue engineering studies. There is, however, a lack of standardized procedures for using this technique. In addition, many types of fluorochromes exist and one could be confused upon selecting the appropriate type, the appropriate concentration, the route of administration, and methods of visualization. All these variables can potentially affect the outcome during fluorescence microscopy. This work aims at providing the bone tissue engineering researcher with an overview of the history, working mechanism, and the potential pitfalls in the use of fluorochromes in animal studies. Experiments using some of the more frequently used fluorochromes are explained and illustrated.