The frequent outbreaks of water and food-borne pathogens pose a high risk to human health. Enterotoxigenic Escherichia coli (ETEC) is one of the pathotype of E.coli responsible for diarrheal diseases like Traveler‘s diarrhea.The severity of infections point towards the need for strict monitoring and translational approach for development of on-site detection system. In the present study, a chip PCR based modular system, which is simple, quicker, costs-effective and suitable for the automated analysis of DNA of selected pathogens such ETEC was explored. The observations made with chip PCR were found to be in concurrence with quantitative PCR in terms of sensitivity and specificity. The use of stationary PCR chip for the gene-specific identification of the ETEC validates a key component towards development of an on-site detection system for water and food borne bacterial pathogens. The chip PCR can be coupled to DNA chips for electrical detection or visual formats for on-site colorimetric detection of PCR products to avoid sample transport and analysis in a reference laboratory for better management of diarrheal diseases.