A major drawback of waste water irrigation to vegetables is the presence of lethal disease causing bacteria and the risk of their transmission to the tomato fruit. The presence of S. enterica subspecies enterica in fruiting bodies of tomato plant was traced, irrigated with contaminated waste water. Molecular and cultural diagnosis of S. enterica subsp. enterica was carried out in tomato fruits after contaminated waste water irrigation to determine its transmission from water to tomato fruits. Sixteen genotypes were irrigated with waste water from germination to maturity. Tomato fruits were sampled and their flesh was used as inoculums for culturing the bacteria. No bacterial infection was detected in two genotypes while remaining fourteen accessions were found positive for bacterial growth in the culture. PCR amplification of bacterial 16srRNA was observed in all 14 genotypes depicting the bacterial infection in these fruits. But the diagnostic primers of S. enterica were amplified only in the fruits of two genotypes out of total 16. These Results showed that 87.5% genotypes were free of S. enterica subsp. enterica contamination, depicting that most of the time pathogen was physiologically blocked from gaining access to the tomato fruit. It further confirmed the presence of variability for the potential of bacterial transmission from root to fruit in the tomato genotypes. The advantage of this variability can be harnessed in the form of breeding such genotypes, which present strong physiological barrier and defence system for the bacterial transmission to the tomato fruit.