Abstract: An automated system and method for chromosome microdissection involves securing a micro-tool, verifying a micro-tip position and configuration and execution of a predetermined cut pattern of a location identified by an equipment operator. The present method involves preparation of sample material on a slide placed upon a stage of an inverted optical microscope, location of the target sample for dissection, micro-tool calibration and microdissection itself. Micro-tool calibration involves the use of cameras, preferably mounted at an angle from each other, for seeing the micro-tool point, such cameras associated with vision software programs capable of locating the tool point tip at three-dimensional space. Microdissection is performed on an isolated section of chromosome placed within the appropriate three-dimensional stage. The present system and method provides reliability and ease of operation thus making microdissection widely available to laboratories.