Many applications of microwave energy to wooden materials have been developed in the last few decades, both for treatment and for diagnostic purposes. All these applications require a reliable estimation of the permittivity of the wood species of interest, which is the physical parameter of crucial importance in the absorption of electromagnetic energy. This paper presents results obtained in the dielectric characterization of five wood species in the frequency range from 2 to 3 GHz, including the ISM frequency of 2.45 GHz. Permittivity was measured by an open-ended coaxial-line probe of new design on wood samples conditioned at several moisture levels. The influence of the natural variability of wood characteristics on the measured permittivity was also investigated by a suitable experimental setup consisting of a poplar table including both sapwood and heartwood regions. Finally, a theoretical discussion on the meaning of a scalar measurement on anisotropic dielectrics is conducted in terms of an isotropic-equivalent permittivity, which is related to the permittivity tensor of the dielectric material.