Many researchers are investigating the extreme resilience of bacterial endospores against chemical and physical inactivating agents. The presence of vegetative cells in spore suspensions can result in overly optimistic assessment of inactivating agents; therefore, various spore purification methods have been applied to separate spores from vegetative cells prior to testing. The present study was undertaken to evaluate the effect of two widely used spore purification methodologies on spore integrity and susceptibility to ultraviolet-A (UVA) radiation and free radicals generated from photocatalysts. Bacillus subtilis and Bacillus cereus spores were purified by procedures that involved heat shock alone or chemical washes, lysozyme treatment and heat shock (CLH). The purified spores were exposed to UVA radiation or free radicals generated by photocatalyst and susceptibility were evaluated in terms of survival ratio. The effect of purification procedure on the spore morphology was investigated with electron microscopy. The CLH purification process significantly damages spore coats and increases the susceptibility of Bacillus spores to UVA radiation and photocatalytic inactivation. It is therefore likely that the survival of CLH treated spores in extra-terrestrial environments would be less than that of the same spores purified by a less aggressive procedure.