An ever more challenging problem in neurobiology will be to identify distinct subpopulations of neurons to study their function in neuronal circuit assembly and function. In order to be able to visualize subpopulations of neurons and distinct subcellular compartments within those neurons we have taken a mouse genetics approach. We have used different spectral variants of the enhanced green fluorescent protein (eGFP) and have made fusion constructs to target the resulting proteins to distinct subcelluar locations. These fusion proteins include the generation of a construct to tag eGFP to membranes by linking an amino-terminal membrane tagging extension to eGFP and the generation of a construct in which eGFP is fused to Synaptophysin to label presynaptic structures selectively. We have used these fusion constructs to generate transgenic mice in which these genes are expressed under the control of Tau or Thy1 regulatory elements to achieve neuron specific expression at different developmental stages. Moreover, we have used the same strategy to express these fusion proteins conditionally by using a Cre-LoxP based genetic system in the mouse. We have tested our strategy extensively in the spinal cord and dorsal root ganglia (DRG) neurons and results from this analysis will be presented. In summary, the combination of conditional activation of eGFP based reporters by Cre recombinase represents a powerful approach to label distinct subpopulations of neurons.