OBJECTIVES: To evaluate the clinical outcome and H. pyloriinfection status by GLQI and PCR, before and after the triple (CMO, CAO or LTC) treatment regimen. METHODS:   Salivary samples of 225 patients of acid peptic disease were used to determine the infection status and GLQI score before and after treatment regimen. Information regarding direct/indirect costs incurred, clinical outcome and side effects of drugs were determined by interviewing the patient and validated questionnaires. RESULTS: Infection status was determined by successful amplification of 16s r RNA and Cag T genes Positive eradication rate was 72.7% in males and 70% in females in CMO treated, 88.13% in males and 87.5% in females in CAO treated and  84.44% in males and 96.67% in females in  LTC treated patients. The highest improvement in the GLQI score after the treatment regimen was visible in the LTC treated group with a change of 65.39, followed by CAO treated patients with a change of 49.73 and CMO treated patients with an improvement of 32.18. The average cost effectiveness ratio was found to be best in the CAO treatment regimen with a ratio of 9.43 followed by LTC treatment regimen with a ratio of 11.74 and CMO with a ratio of 49.13. Side effects like diarrhea, nausea, bad taste and metallic taste were significantly enhanced in CMO (P <0.001) when compared to CAO and LTC treatment regimens. CONCLUSIONS: The present investigation suggests that LTC has better efficacy and safety profile, but CAO is most cost effective amongst the three treatment regimens. PCR assay can be scaled up for hospitals or clinics as a cost effective non invasive diagnostic test.