We developed a multicolor neuron labeling technique in Drosophila melanogaster 
that combines the power to specifically target different neural populations with 
the label diversity provided by stochastic color choice. This adaptation of 
vertebrate Brainbow uses recombination to select one of three epitope-tagged 
proteins detectable by immunofluorescence. Two copies of this construct yield 
six bright, separable colors. We used Drosophila Brainbow to study the 
innervation patterns of multiple antennal lobe projection neuron lineages in the 
same preparation and to observe the relative trajectories of individual 
aminergic neurons. Nerve bundles, and even individual neurites hundreds of 
micrometers long, can be followed with definitive color labeling. We traced 
motor neurons in the subesophageal ganglion and correlated them to neuromuscular 
junctions to identify their specific proboscis muscle targets. The ability to 
independently visualize multiple lineage or neuron projections in the same 
preparation greatly advances the goal of mapping how neurons connect into 
circuits.