This paper presents a color stereo matching method. We first show the effect of using color information in stereo matching mathematically by using sum-of-squared-differences (SSD) criterion and then experimentally by using synthesized images. We then present a color stereo matching algorithm for a medical application. The algorithm takes into account both the intensity and the disparity variations within the matching window, and estimates the disparity at subpixel resolution exploiting color stereo images. We have applied the algorithm to three-dimensional measurement of optic nerve heads using stereo fundus images. The experimental results show that the proposed stereo algorithm together with various means of displaying the results could give useful information for diagnosing and monitoring glaucoma.