Androgen withdrawal is the standard of care for men with metastatic prostate cancer. Whilst all patients initially respond, resistance is inevitable and lethal castration-resistant prostate cancer ensues. Using patient-derived xenografts (PDX) of localised tumours, we have identified a sub-population of castration-tolerant prostate cancer cells that survive following castration. Identifying the unique biological characteristics of these cells is essential in determining their role in tumour progression and potential to be targeted by therapeutic agents. To study the genomic features of castrate-tolerant cells, we enriched for prostate cancer cells from PDXs using FACS and subjected them to single cell isolation and RNA seq. We efficiently captured and sequenced > 50 cells from pre- and post-castration PDXs using the Fluidigm C1 platform. Sequencing of isolated single cells was performed using the Illumina HiSeq in rapid mode with 50 bp fragment sequencing chemistry (3Million reads/cell). Multidimensional scaling showed that the response to castration is not uniform in all human cells. A unique gene set was identified in intact versus castrate-tolerant cells; we identified distinct changes in energy metabolism, including suppression of ATP production to aid cell survival. We also detected consistent up-regulation of the retinoic acid signaling pathway, involving up-regulation of CRABP2 and RARRES3 expression in castrate-tolerant cells. This is the first study to report of gene expression in single human prostate cells and revealed novel endocrine-related changes prior to and following androgen deprivation. Our data suggest that further and/or alterative hormone suppression may be effective in targeting castration-tolerant prostate cancer cells.