This paper describes the automation of an extraction line and mass spectrometer for the determination of noble gas isotope concentrations in rock and mineral samples, housed in the Isotope Geochemistry Facility at Woods Hole Oceanographic Institution (WHOI). The gas extraction occurs in an automated ultra-high-vacuum system designed and fabricated at WHOI. The noble gases of interest are extracted in vacuo by crushing or high temperature fusion, separated using a cryogenic charcoal trap (operated between 7 degrees and 300 degrees K), and delivered to a Mass Analyzer Products 215-50 mass spectrometer for measurement of isotopic composition. The system is controlled by a PC running under the Windows NT operating system. The software, largely written in Visual Basic and developed at WHOI, provides for synchronization of the extraction process with the mass spectrometer measurements. The extraction line control software is written so that the user can easily modify and customize the procedures, and allows automated operation. The extraction line software also provides a test scheduler, with building blocks which allow control of the system hardware by the computer without programming, for modification and extension of the system by the operators. Software on a second PC controls the operation of the mass spectrometer over an IEEE-488 (GPIB) bus. This code was modified at WHOI to provide for the synchronization of the mass spectrometer with the extraction line and to optimize the determination of the measured gas concentrations. The system is primarily used to make helium and neon isotope measurements, in full 24 hour automation mode, but has also been designed and tested for Ar and Xe isotopes. This system is devoted to the measurement of both mantle and cosmic-ray-produced noble gas isotopes. He and Ne isotopes are useful tracers of mantle evolution and degassing and are measured at low levels in oceanic basalts. Cosmogenic He-3 and Ne-21 can be used to measure surface exposure ages, which has wide application to quaternary geology, volcanology, and geomorphology.