The refractive index is an important property affecting aerosol optical properties, which in turn help determine the aerosol direct effect and satellite retrieval results. Here, we investigate the real refractive indices (m(r)) of secondary organic aerosols (SOA) generated from the photooxidation of limonene and a-pinene with different HC/NOx ratios. Refractive indices were obtained from polar nephelometer data using parallel and perpendicular polarized 532 nm light combined with measured size distributions, and retrievals were performed using a genetic algorithm and Mie-Lorenz scattering theory. The absolute error associated with the mr retrieval is +/- 0.03, and reliable retrievals are possible for mass concentrations above 5-20 mu g/m(3) depending on particle size. The limonene SOA data suggest the most important factor controlling the refractive index is the HC/NOx ratio; the refractive index is much less sensitive to the aerosol age or mass concentration. The refractive index ranges from about 1.34 to 1.56 for limonene and from 1.36 to 1.52, for alpha-pinene, and generally decreases as the HC/NOx ratio increases. Especially for limonene, the particle diameter is also inversely related to the HC/NOx ratio; the final size mode increases from 220 to 330 nm as the HC/NOx ratio decreases from 33 to 6. In an effort to explore the ability of models from the literature to explain the observed refractive indices, a recent limonene oxidation mechanism was combined with SOA partitioning and a structure property relationship for estimating refractive indices of condensing species. The resulting refractive indices fell in a much narrower range (1.475 +/- 0.02) of mr than observed experimentally. We hypothesize the experimentally observed high mr values are due to oligomerization and the low values to water uptake, small soluble molecules such as glyoxal and other factors, each of which is not included in the oxidation mechanism. Aerosol formation yields were measured over the mass concentration range from 6 to similar to 150 mu g/m(3), over which they increased steadily, and were higher for high HC/NOx ratio experiments.