A laser eye surgery system focuses light along a beam path to a focal point having a location within a lens of the eye. The refractive index of the lens is determined in response to the location. The lens comprises a surface adjacent a second material having a second refractive index. The beam path extends a distance from the surface to the focal point. The index is determined in response to the distances from the surface to the targeted focal point and from the surface to the actual focal point, which corresponds to a location of a peak intensity of an optical interference signal of the focused light within the lens. The determined refractive index is mapped to a region in the lens, and may be used to generate a gradient index profile of the lens to more accurately place laser beam pulses for incisions.