Lineage-tracing experiments aim to identify and track the progeny and/or fate of cells. The use of inducible recombinases and fluorescent reporters has been instrumental in defining cellular hierarchies and allowing for the identification of stem cells in an unperturbed in vivo setting. The refinement of these approaches, labeling single cells, and the subsequent quantitative analysis of the clonal dynamics have allowed the comparison of different stem cell populations as well as establishing different mechanisms of cellular replenishment during steady-state homeostasis as well as during morphogenesis and disease. Utilizing this approach, it is now possible to establish the cellular hierarchy in a given tissue and the frequency of cell fate decisions on a population basis, thus providing a comprehensive analysis of cellular behavior in vivo. Although in this chapter we describe a protocol for lineage tracing of cells from fetal intestinal epithelium to the adult intestine, this approach can be widely applied to quantitatively assess the cell fate of any fetal cell during morphogenesis.