Subsurface horizontal flow constructed wetlands (HFCW) and vertical flow constructed wetlands (VFCW) have been compared regarding their efficiencies on microbiological indicators removal. Seven types of HFCWs and two types of VFCWs have been monitored for several years. Fecal coliforms, E. coli, somatic coliphages and F-specific bacteriophages were analyzed in the influent and effluents of each system. All constructed wetlands monitored were planted with Phragmites australis but have different design characteristics and operation variables. All data were statistically treated (SPSS v17) in order to analyse the effect of design and operation variables on each microbiological indicator. VFCWs were more efficient than HFCWs systems when considering removal rates per surface for all the microbiological indicators (cfu or pfu removed/m2.d). Nevertheless, considering mean removal efficiencies (in log units), results did not show statistically significant differences. The hydraulic retention time was the key parameter regarding filter disinfection capacity in both types of filters. Bacterial indicators were removed at a higher rate than viral indicators.