Studies on the formation of connections in the developing nervous system are greatly aided by methods that permit the differential visualisation and manipulation of pre- and postsynaptic partner neurons. This has been facilitated by the advent of the LexA-based, GAL4/UAS-independent, binary expression system. On the molecular side, the introduction of DNA sequences into expression vectors has been simplified by the Invitrogen Gateway cloning technology. We have developed cloning vectors that combine the Gateway cloning technology with the LexA-based genetic expression system. These vectors facilitate the creation of driver and reporter constructs for the generation of Drosophila transgenic lines for the new LexA-based binary transcriptional system. We further report a new LexA::GAD sensory neuron driver and a red fluorescent membrane targeted lexAop reporter designed to complement the existing GFP-based lexAop reporter. Using these transgenic lines we have been able to differentially label motor and sensory neuron projections in the ventral nerve cord of Drosophila larvae.