The effect of non-ideal cylindrical diffusers on the fluence rate distribution is studied in intraluminal and interstitial light delivery settings. Two types of diffuser non-uniformities are modeled: a forward-directed polar emission profile, and a longitudinal emission profile with a peak at the distal tip of the diffuser. These effects were compared with an ideal diffuser constructed via a superposition of isotropic point sources placed along the length of the diffuser. Monte Carlo simulations were run for a wide range of optical properties and the resulting fluence rate distribution were analyzed. Parameters describing the shape of these distributions were defined. The longitudinal profile most strongly influenced the shape of the fluence rate distribution displaying high local fluence rates, high degrees of asymmetry, and deeper penetration into tissue. These characteristics are particularly evident for interstitial illumination. In intraluminal illumination, both non-ideal profiles produced a shift of the fluence rate, but, while remaining largely insensitive to optical properties for the longitudinal diffuser, the position of the peak fluence rate varied to a considerable extent for the polar anisotropic diffuser, particularly as a function of albedo. Measurement of the polar emission profile and its inclusion in treatment planning, based on the tissue optical properties, is recommended for the intraluminal geometry. The longitudinal emission profile should be determined regardless of the application, together with knowledge of the tissue optical properties.