In this work, the disinfection efficiency of water and secondary treated wastewater by means of UV-A, UV-C and solar irradiation in the presence or absence of TiO(2), using a reference strain of Enterococcus faecalis as faecal indicator, was evaluated. Operating parameters such as TiO(2) loading (0-1500 mg L(-1)), initial bacterial concentration (2 × 10(2)-10(8) CFU mL(-1)) and treatment time (up to 120 min) were assessed concerning their impact on disinfection. E. faecalis inactivation was monitored by the conventional culture method and real-time PCR. Regarding photocatalytic treatment, disinfection efficiency was improved by increasing TiO(2) concentration and bacterial inactivation took place in relatively short treatment times. Comparing the three disinfection methods, it was observed that UV-C irradiation yielded a better efficiency during water treatment than UV-A and solar irradiation. Furthermore, UV-A was more efficient than solar irradiation in the presence of the same loading of TiO(2). Regarding real wastewater, it was observed that only UV-C irradiation was capable of totally inactivating E. faecalis population in a short time. Screening the results obtained from both applied techniques (culture method and real-time PCR), there was a discrepancy, regarding the recorded time periods of total bacterial inactivation. Real-time PCR data revealed that longer periods are needed for 100% bacterial reduction during the treatments tested compared to the estimated time by culture method. This is probably attributed to the phenomenon of "viable but not culturable bacteria", caused by stressed conditions induced during disinfection experiments. Taking into account the contrast of results and in order to perform a thorough evaluation of disinfection techniques, conventional culture method should be accompanied by a DNA-based method. According to our findings, real-time PCR proved to be a reliable and accurate molecular tool for the identification and quantification of bacterial indicators, like E. faecalis, in aquatic samples after disinfection treatment.