The zebrafish has emerged as a powerful model to study organ development and regeneration. It has a number of advantages over other vertebrate model systems. The embryo can be kept transparent throughout embryonic development, which allows direct visualization of the developing organs. In addition, embryos can be easily manipulated surgically, genetically, or chemically. Furthermore, because nephron shape and function are remarkably conserved among vertebrates, zebrafish findings can directly inform human studies. Here, we describe a simple procedure that can be used by laboratories to investigate the development of zebrafish kidney and other organs by time-lapse microscopy.