The present invention provides a method for inactivating pathogens in a body fluid, such as plasma, red cells, platelets, leukocytes, and bone marrow. The present invention minimizes adverse effects caused by the photosensitive agents while retaining the disinfecting activity of such agents and processes. Pursuant to the present invention, prior to irradiating a body fluid including a photoactive drug, the extracellular fluid, which in the case of blood components includes plasma proteins is at least substantially reduced. Additionally, after the irradiation process, the resultant body fluid is prevented from contacting additional extracellular fluid, e.g., plasma proteins, for a predefined period.