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Abstract: In this contribution we present results from two individual gas monitoring experiments which were conducted during the drilling of the SAFOD (San Andreas Fault Observatory at Depth) boreholes. Gas from circulating drilling mud was monitored during the drilling the SAFOD III side tracks and was later analyzed for δ13C (CH4, C2H6 and C3H8), H/D (CH4) and noble gas isotopes. Furthermore, gas accumulations induced by drill pipe retrieval (“trip gas”) from the SAFOD MH and the SAFOD III boreholes were also investigated. The data are interpreted in the context of gas migration processes and the permeability structure of the San Andreas Fault (SAF) around two actively deforming zones at 3194m and 3301m borehole depth. Helium isotope ratios of 0.86 Ra at 3203m and between 0.51 and 0.88 Ra at 3262m (Ra is the atmospheric 3He/4He ratio) indicate an improved flow of mantle volatiles between both fault strands. Much lower values were observed at 3147m (0.26 Ra) and 3312m (0.22 Ra). Hydrocarbon concentrations coincide with the occurrence of shale at ~3150–3200m and below ~3310m depth. The molecular and isotope composition of hydrocarbons and their spatial distributions imply hydrocarbon generation by thermal degradation of organic matter followed by extensive diffusion loss. Carbon isotope data furthermore suggest a thermal maturity of the source rock of approx. 1.4%R0. The concentration of trip gas is generally low in the interval 3100m–3450m but exhibits high spatial variability. At 3128m and 3223m depth, the trip gas concentrations are as low as in the granite section of the SAFOD Main Hole. Considerable variations of Ra values, trip gas concentrations, and the molecular composition of hydrocarbons when penetrating the active fault strands let us conclude that the permeability of the fault transverse to the fault direction is limited and that the active fault has not been breached over many earthquake cycles such that little or no fluid exchange took place. Diffusion is the dominant mechanism controlling hydrocarbon migration through the fault strands. The elevated Ra values between both fault strands may reflect either episodic or continuous flow of mantle-derived fluids, suggestive of some limited permeability parallel to the fault direction. [Copyright &y& Elsevier]