Shortly after the initial demonstration of the feasibility of gene analysis at the single cell level,1 the two major technical trends enabling gene expression analyses of single cells developed in the early 90s. These developments were aimed either at whole transcriptome analysis based on RNA amplification,2,3 or at limited gene expression profiling using RT-PCR for correlating molecular and functional properties.4 The brain complexity and cellular diversity has been a strong incentive for the development of these tools at a time when many of the major constituents of neurotransmission had been cloned. Both techniques initially relied on the use of the patch-clamp technique5 to harvest selectively the cell's mRNAs. In this chapter we will detail the key steps, which assessed the reliability and functional relevance of the “single cell RT-PCR after patch-clamp” technique (scPCR, Lambolez et al., 1922), and describe its evolutions. We will also share our observations on the design and interpretation of scPCR experiments and discuss the limits of this approach.