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Gastropanel, serological ELISA test comprising of stomach biomarkers; serum pepsinogen I, pepsinogen II, gastrin-17, and Helicobacter pylori antibody depicts clearly the morphological and functional status of stomach mucosa in patients suffering from dyspepsia. Although the traditional system of medicine is a huge resource of efficient formulations useful in gastrointestinal disorders such as functional dyspepsia, lack of robust scientific evidence, and qualitative/subjective parameters like symptom scores do not suffice the need for the same. This study was thus planned to assess usefulness of gastropanel tests to validate efficacy of Avipattikar choorna, well-known antacid remedy in functional dyspepsia. A. choorna was given to patients of dyspeptic disorders following which gastropanel was performed pre- and post-treatment. The gastropanel findings obtained, prior and post-interventions were compared using Wilcoxon MPSR test and a level of P < 0.05 was considered for statistical significance. It was observed that although symptom scores showed improvement in all patients after treatment, change in pre- and post-values of gastropanel was seen only in few patients. Gastropanel could differentiate between true responders and non-responders, identification of which was difficult merely with symptom scores. Another highlight was that A. choorna proved more effective in H. pylori IgG positive cases. Gastropanel may be used as an effective tool to understand and validate the efficacy of traditional medicines in functional dyspepsia and gastric disorders along with its effect on stomach physiology and acid regulation. Need for employment of quantitative/objective parameters for traditional system drugs validation is also highlighted.