Mesencephalic dopaminergic neurons (DA) present two major groups of projecting cells: the A9 neurons of the Substantia Nigra (SN) that are involved in regulating voluntary movements and postural reflexes and the A10 cells of the Ventral Tegmental Area (VTA) that play a fundamental role in reward and attention. Selective degeneration of A9 cells leads to Parkinson's disease (PD). Full length cDNA cloning, tiling arrays and high-throughput sequencing have been proving that a much larger portion of the genome is transcribed. However, due to the heterogeneity of neuronal cell types in the brain, the structure of the transcriptome of a specific class of neuron remains unclear. We thus combined transgenic labeling, Laser Capture Microdissection and gene expression profiling to describe the transcriptional landscape of mesencephalic dopaminergic neurons. To this purpose we resorted to three platforms: the SISSA-RIKEN cDNA microarrays, exon arrays from Affymetrix and nanoCAGE (Cap Analysis Gene Expression), a new technology that takes advantage of second generation sequencing for mapping TSSs from small amounts of starting material. Together with the identification of the expression of alpha and beta- chains of hemoglobin, we have described the transcriptome of DA neurons with special attention to alternative TSSs usage, gene networks discovery, antisense transcription and expression of repetitive elements.