The optical waveguiding capabilities of polycyanurate thermoset nanorod (PCNs) arrays mounted on planar gold substrates were investigated using optical waveguide spectroscopy (OWS). The nanorods, with diameter of 60 and 150 nm, and length of 650 nm, are formed by thermal polymerization of cyanate ester oligomers within porous anodic aluminium oxide templates. We discuss the waveguiding properties of the PCNs arrays when the nanorod diameter is much smaller (<1/10) than the wavelength of the guided light. We monitored the changes in the waveguiding modes by exchanging the interrod filling environment with water, ethanol, and isopropanol. This study led to a sensing figure of merit as high as 196 reciprocal refractive index units, which is higher than that of other previously studied sensors based on angular modulation. Furthermore, numerical simulations were performed by applying an Effective Medium Theory (EMT) based on the Maxwell‐Garnett approximation for the prediction of the optical properties of anisotropic nanorod arrays. Simulations based on Fresnel equations were used for estimating the optimal fabrication geometry, with varying the nanorod diameter and the interrod distance. Based on these results, we introduce the applicability of the PCNs arrays platform as a concept in optical biosensors and other related applications (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)