Light of certain wavelengths can be used to inactivate pathogens. Whole blood is opaque; thus, the penetration of light is reduced. Here, we overcame this limitation using a thin transparent tube that is illuminated from all angles. Three light‐based techniques were evaluated: photodynamic therapy (PDT) using a 660‐nm light and antibody‐photosensitizer conjugates, ultraviolet, and violet light. We observed a reduction of 55–71% of Staphylococcus aureus after 5 h of exposure (starting concentration 10⁷ CFU mL⁻¹) and an 88–97% reduction in methicillin‐resistant Staphylococcus aureus (MRSA) (starting 10⁴ CFU mL⁻¹). An 83–92% decrease for S. aureus and 98–99.9% decrease for MRSA were observed when combined with an immunocapture approach. Complete blood count with differential analysis did not reveal any significant changes in the blood cell numbers. Genotoxicity studies showed that violet and ultraviolet did not induce any significant level of single strand breaks and alkali labile sites in the peripheral blood mononuclear cells (PBMC). In contrast, ultraviolet did induce a very low level of cyclobutane pyrimidine dimers, a UV damage indicator. PDT generated a significant level of single strand breaks and 8‐oxoGua in these cells. The approaches showed promise for whole blood pathogen inactivation with minimal collateral damage to PBMC.