We have used ellipsometry to study oligonucleotides bound on an array by observing changes in the optical thickness of the organic material attached to the surface. Interferometry has been used as a complementary technique to confirm our ellipsometry measurements. We have used these optical methods to characterize the chemical steps involved in synthesizing oligonucleotides on a solid support. Large area arrays have been mapped by ellipsometry with a spatial resolution of similar to 1 mm(2) and a sub-nanometer optical thickness resolution. We have demonstrated that this method can differentiate between areas containing oligonucleotides of different lengths.