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Objectives The aim of our study was to describe the scintigraphic patterns of 99mTc-pertechnetate uptake in patients who were referred to the department of nuclear medicine for evaluating and diagnosing ectopic gastric mucosa in foregut and midgut duplication cysts. Materials and methods This hospital-based, retrospective cum prospective research spans a period of 8 years from April 2014 to January 2022. Previous hospital medical records were analyzed and subsequently, a database was prepared which included the age, sex, clinical indication of a 99mTc-pertechnetate scan, and the planar and SPECT-computed tomography (CT) imaging findings. Postoperative histopathological reports were available for 21 patients. Dynamic and planar static imaging was performed. We included SPECT-CT in suspected duplication cysts to increase the sensitivity and specificity which is a tradeoff for a small amount of additional radiation exposure. A total of 69 patients were subjected to a 99mTc-pertechnetate scan for suspected foregut or midgut duplication cysts. All were subjected to dynamic planar and delayed static images up to 24 h or until focal uptake of radiotracer was noted which corroborated the anatomical findings, whichever was earlier. SPECT-CT was performed along with the planar study in 31 patients which confirmed the findings. Previously performed CT scans were used for anatomical correlation in the remaining ones Results Duplication cysts were localized in a total of 28 patients (19 foregut duplication cysts and 12 small bowel duplications – 3 patients had dual duplication cysts, both foregut, and midgut). Forty-one patients had no scintigraphic evidence of ectopic gastric mucosa. Of these 69 patients, histopathological diagnosis was available for 21 patients (22 lesions). The report was concordant with the scan findings in 15 patients (16 lesions) and 6 patients showed discordance in histopathological diagnosis and scan findings. Conclusion In conclusion, multi-time point imaging is the key to diagnosing ectopic gastric mucosa of various sizes and in various locations. An abnormal radiotracer uptake in dynamic sequences, even before the appearance of the stomach in the region of the small bowel is indicative of intestinal duplication, and delayed radiotracer visualization in the region of the thorax is characteristic of intrathoracic foregut duplication cyst.