Methods for reducing the pathogen content of a biologically derived composition by illuminating the composition with at least one high-intensity, short duration pulse of incoherent polychromatic light in a broad spectrum. In the resultant treated compositions, biomolecules of interest remain biologically active. The content of pathogens, such as viruses, bacteria, pyrogens, fungi and / or prions, present in a biologically derived composition, such as blood serum, blood plasma or other blood product, including, insulin, transferrin, heparin, collagen, Factor VIII and / or Factor IX, or a composition containing monoclonal antibodies, proteins from genetically engineered cell lines or the like, is reduced by illumination with broad-spectrum pulsed light. The content of HIV-1, SV40, canine parvovirus or bovine viral diarrhea virus in a biologically derived composition is dramatically reduced with a single pulse of broad-spectrum light.