Disclosed are methods and apparatus for safe, simple and effective broad-spectrum treatments of chronic rhinosinusitis and other common and less common infections of the sino-nasal tract which may implicate not only a wide range of bacterial species but also fungi and viruses. Electromagnetic radiative energy including visible, and optionally, thermal RF, microwave or other longer wavelengths, is applied to target internal surfaces of the sino-nasal tract to destroy or incapacitate superficial microorganisms without the use of antibiotics. The treatment can be controlled to permit regrowth of healthy microflora. A handheld energy applicator has a light output head receivable into, or engageable with, the treatment subject's nostril which may be provided with extensions to reach the sinuses. Useful embodiments of the invention include pretreatment of target sino-nasal surfaces with a photosensitizing agent such as an oxidizing agent or a complementary stain. For example methylene blue can be used with orange or red light. The combination treatment of photosensitizer and application of visual wavelength energy provides a flexible treatment regimen which enables low concentrations of stains to be employed, minimizing aesthetic problems.