This document summarizes the development of an automated filter-based system for isolating and detecting circulating tumor cells (CTCs) from blood samples. The system uses size- and deformability-based filtration to recover over 90% of CTCs while depleting over 99.99% of white blood cells. It also allows identification of protein markers on CTCs through immunostaining and detection of as few as 5 CTCs through quantitative RT-PCR analysis. Optimal sample storage conditions of 23°C for up to 72 hours was also determined.