Using scanning confocal microscopy, we measure the backscattered second harmonic signal generated by a 100 fs laser in rat-tail tendon collagen. Damage to the sample is avoided by using a continuous scanning technique, rather than measuring the signal at discrete points. The second harmonic signal varies by about a factor of 2 across a single cross section of the rat-tail tendon fascicle. The signal intensity depends both on the collagen organization and the backscattering efficiency. This implies that we cannot use intensity measurements alone to characterize collagen structure. However, we can infer structural information from the polarization dependence of the second harmonic signal. Axial and transverse scans for different linear polarization angles of the input beam show that second harmonic generation (SHG) in the rat-tail tendon depends strongly on the polarization of the input laser beam. We develop an analytical model for the SHG as a function of the polarization angle in the rat-tail tendon. We apply this model in determining the orientation of collagen fibrils in the fascicle and the ratio γ between the two independent elements of the second-order nonlinear susceptibility tensor. There is a good fit between our model and the measured data. © 2002 Society of Photo-Optical Instrumentation Engineers.