BrdU is a thymidine analog that is incorporated into DNA during the S-phase of the cell cycle. BrdU incorporation can be used to quantify the number of cells that are in S-phase in the time period that BrdU is available. Thus, BrdU incorporation is an essential method in the quantitative analysis of cell proliferation, during normal embryonic development or after experimental manipulation. It is a reliable and versatile method that can be easily combined with immunohistochemistry and in situ hybridization to relate cell proliferation with gene expression. BrdU incorporation has been used in all model organisms; here, we describe a protocol adapted for use in Xenopus embryos.