Single-cell analysis reveals the underlying heterogeneity and biological complexity present within cell populations. Fluidigm offers specialized microfluidic tools for single-cell capture and molecular analysis, making this approach tractable for all researchers. The Fluidigm C1 Autoprep System captures individual single cells and prepares them for either targeted gene expression analysis (RT-PCR), whole transcriptomes analysis (RNAseq) or whole genome amplification (WGA) in a highly automated and controlled fashion. An overview of these tools and protocols will be presented, along with recently generated local customer data measuring single cell gene expression in human breast adenocarcinoma cells.