Catheter-based systems for in-vivo targeted light therapy include a first type of catheter configured for photo-activating photosensitive substances in tissue, and a second type of catheter configured for photo-degrading photosensitive substances in tissue. The catheters may be configured to produce light using a variety of light sources, such as light emitting diodes (LEDs) and fiber optics. The light transmission is directed to tissue in such a way that only portions of tissue in a treatment area are exposed to light, depending upon whether the tissue is diseased or healthy.