In the framework of the Cajon Pass scientific drilling project in the vicinity of the San Andreas fault system, petrophysical analysis of the retrieved core was focused on elastic properties, density, porosity, and permeability. Simultaneous study of rock mineral composition, texture, degree of metamorphism, and fracture drilling yielded a petrophysical classification of the studied rock that is convenient for the interpretation of the downhole logging data. Given the small percentage of the hole drilled with coring, the geophysical data were used to construct a lithologic-petrophysical column of the well. Most of the petrophysical variability seen in this column is the result of laumontite alteration of granitoids during retrograde metamorphism in the zeolite facies. The intensity peaks of the alteration process are spatially confined to the oblique reverse faults (25¿--40¿ dip angles as observed in the core and borehole televiewer images) accompanied by brittle deformation of the adjacent granitoids. The marked drop in density, velocity, and elastic moduli and the noticeable increase in porosity and permeability of these altered fault zone rocks are enhanced owing to in situ stress shielding. The low velocity and density and higher permeability associated with these faults makes them detectable seismic reflectors and hydrologic conduits in the upper crust. By contrast, based on our data analysis, the matrix of the intact crystalline rock in situ is inferred to be essentially free of microcracks and interconnected channels with free water. A detailed analysis of the various factors affecting the microcrack introduction into the cores retrieved from deep and superdeep holes is presented to show that a unique interpretation of in situ stresses from analysis of microcracks in cores is not possible without a better understanding of the mechanisms of crack formation. ¿ American Geophysical Union 1992