Flow cytometry is extensively used for the isolation of discreet populations of cells from complex pools. The advent of autofluorescent (AFP) reporters such as wild type Green Fluorescent Protein (wtGFP) (Chalfie et al., 1994) and its variants, including enhanced green fluorescent protein (EGFP) and enhanced yellow fluorescent protein (EYFP) (Cormack et al., 1996), as vital reporters opens up the possibility of sorting live reporter-expressing cells. Moreover the use of these reporters in transgenics (Okabe et al., 1997) or mice carrying homologously targeted loci (Godwin et al., 1998) should enable the direct isolation of reporter-expressing cells from any desired lineage. Here we have assessed this approach in transgenic mice. ES cell-mediated transgenesis was used for generating a line of mice that express an autofluorescent EYFP reporter in the heart and part of the neural tube at midgestation. Pools of fluorescent cells harboring and expressing the EYFP reporter were isolated from defined regions of embryos and their origin confirmed by assaying the expression of domain-defined marker genes. Such a tool should prove useful for gaining access to any given lineage that can be fluorescent protein reporter tagged.