The disinfection of a continuous flow of an effluent from an advanced primary treatment (coagulation-flocculation-sedimentation) with or without posterior filtration, using either peracetic acid (PAA) or ultraviolet (UV) radiation was studied. We aimed to obtain bacteriological quality to comply with the microbiological standard established in the Mexican regulations for treated wastewater reuse (NOM-003-SEMARNAT-1997), i.e., less than 240 MPN (most probable number) FC/100 mL. The concentrations of PAA were 10, 15, and 20 mg/L, with contact times of 10, and 15 min. Fecal coliforms (FC) inactivation ranged from 0.93 up to 6.4 log units, and in all cases it reached the limits set by the mentioned regulation. Water quality influenced the PAA disinfection effectiveness. An efficiency of 91% was achieved for the unfiltered effluent, as compared to 99% when wastewater was filtered. UV radiation was applied to wastewater flows of 21, 30 and 39 L/min, with dosages from 1 to 6 mJ/cm2. This treatment did not achieve the bacteriological quality required for treated wastewater reuse, since the best inactivation of FC was 1.62 log units, for a flow of 21 L/min of filtered wastewater and a UV dosage of 5.6 mJ/cm2.