The photocatalytic deactivation of Escherichia coli HB101 by two different structures of TiO2, rutile and anatase (used separately and in a 1:1 mixture), was examined. The microorganism was deposited on a filter membrane containing 520 mg/m2 of TiO2 and then irradiated by a neon lamp. In order to study the rate of deactivation of the microorganism we studied four different exposure times: 20, 40, 60 and 90 min. The results showed that rutile has an antimicrobial activity higher than anatase, while the mixture had values near to the average between them in every condition. The highest difference in the inactivation capacity of the two structures is observable at shorter times. The effect of the different crystal phases was evaluated by Scanning Electron Microscopy.