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Background and Aim: Water crisis in many regions of the world especially arid and semi-arid areas such as Iran, is an important obstacle for socioeconomic development and food security. Under such circumstances, wastewater reuse in agriculture can be regarded an important alternative water source. However, treated wastewater may contain some types of pathogenic microorganisms which can threaten human health. In the present study we compared the impacts of treated wastewater (TWW) and tap water irrigation on microbiological quality of soil and crops (maize and maize leaves) through a furrow irrigation system in an experimental field. Materials and Methods: Total and fecal coliforms and Escherichia coliwere monitored as indicator bacteria in TWW, irrigated soil and harvested maize and maize leaves. We investigated the presence of Salmonellaand Shigellaby using a combination of culture and molecular methods. Statistical analyses were performed by SPSS 22.0 software. P<0.05 was considered statistically significant. The Mann-Whitney test was used to evaluate the difference of microbial parameters inthe plots irrigated with the two types of water.Results: The microbiological quality of wastewater in terms of mean concentration ofE. coli(3.5 Log MPN/100 ml) was compatible with that recommended by theworld health organization (WHO) for irrigation offast-growing crops (≤ 105E. coliper 100 ml). Although, the microbiological quality of soil was affected by TWW irrigation (p < 0.05), a relatively low concentration of E. coliwas detected in soil. Harvested maize had no microbial contamination with E. coli. However, one sample of wastewater-irrigated maize leaves was contaminated with E. coli. The TWW, soil and crop samples were not positive for pathogenic bacteria. Conclusion:According to the results, TWW could be used as an alternative source for irrigation of maize.