Adaptability to a broad range of environments together with relatively high resistance to antibiotics and to disinfectants makes Pseudomonas aeruginosa a concern in hospitals and in public health. We investigated whether UVA-mediated photochemical inactivation of P. aeruginosa could be accomplished with high efficiency while at the same time preserving the sensitivity of subsequent diagnostic tests. We characterized dose responses and bactericidal kinetic rates of 5-iodonaphthyl 1-azide (INA) and of amotosalen (AMO) as these substances exposed to UVA are known to inactivate germs with minimal impact to blood products or to viral antigens. Neither UVA without photochemicals nor INA or AMO in the dark inactivated bacteria. We found that AMO was ca 1000-fold more effective in inactivating P. aeruginosa cells than INA under similar conditions. Photoinactivation with either INA or AMO at conditions that abolished bacterial infectivity did not impair polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) testing. For comparison, similar titers of Bacillus atrophaeus spores (a surrogate for B. anthracis) remained unaffected at conditions that reduced the survival of P. aeruginosa below detection levels. The results presented in this study should assist in improved methods to inactivate P. aeruginosa in environmental, clinical and forensic samples without impairing subsequent nucleic acid- or immune-based analysis.