The mechanical and hydraulic properties of many rock masses are affected significantly by the additional mechanical compliance and fluid conductivity that result from joints, fractures or faults. The effects of these features, generally referred to as joints, can be so pronounced in many problems in geology or geophysics, mining or petroleum engineering, hydrogeology and waste management that it is important to be able to locate and characterize them remotely within a rock mass using geophysical methods. The effect of joints on seismic wave propagation, therefore, becomes important also. Experimental measurements of the deformation of natural joints are analyzed in terms of theories concerning the roughness of the two joint surfaces and their deformation under stress. For many rocks, the deformation of the surfaces is reversible after the first few cycles of loading and unloading and is, therefore, elastic. The highly non-linear stress-deformation curves for joints must be a result of changes in the geometry of the areas of contact between asperities brought about by the elastic deformation of adjacent voids in response to changes in the applied stress. The flow of fluids between the surfaces of a joint must also depend upon the geometry of the void space between these surfaces. Measurements using liquid metal porosimetry, show that when the two surfaces of a natural joint are in contact with one another, this geometry becomes so complex that fluid through the joint cannot be approximated as laminar flow between parallel surfaces leading to a cubic relation between flux and aperture. At low stresses, fluid flow through a joint decreases much faster than the cube of the joint closure. This is shown to be a result of changes in contact area, tortuosity and hydraulic aperture brought about by deformation of the void space between the two surfaces of the joint. At high stresses, fluid flow through a joint asymptotes to an irreducible level, largely independent of joint closure and further changes in stress. The slope of a tangent to the curve relating the average closure between the two surfaces of a joint to the stress across the joint defines a specific stiffness for the joint at that stress. The effect of joints on seismic waves can be analyzed by using this specific stiffness as a boundary condition in the seismic wave equation. Displacements across this boundary are discontinuous while stresses are continuous. Although the specific stiffness of the joint and the properties of the rock on each side of it are assumed to be completely elastic, the displacement discontinuity leads to frequently-dependent reflection and transmission coefficients for compressional and shear waves as well as frequency-dependent group time delay for the transmitted waves. This concept can be extended to include a velocity discontinuity across the joint, where the contained fluid or the properties of the rock provide viscous as well as elastic coupling across a joint. Theoretical predictions based on the displacement discontinuity and velocity discontinuity theories agree very well with the results of laboratory measurements of seismic pulses transmitted across natural joints with different specific stiffnesses.