Fluoroscopic examinations like Endoscopic Retrograde Cholangiopancreatography (ERCP) and Percutaneous Transhepatic Cholangiography (PTC) are fundamental in diagnosing and treating hepatobiliary diseases. However, these procedures expose patients to significant radiation, highlighting the need for a detailed assessment of the radiation doses received by critical organs. The study’s primary objective is to determine the experimental doses received by critical organs in patients undergoing these procedures. This study utilized an Alderson RANDO phantom outfitted with Thermoluminescent Dosemeters (TLDs) to experimentally measure the radiation doses received by various organs during ERCP and PTC procedures. This method provided direct and accurate data on organ-specific radiation exposure, contrasting with the traditional approach of relying on theoretical simulations. The analysis revealed that PTC generally results in higher radiation doses to organs compared to ERCP. Critical organs, such as the thyroid, spleen, liver, pancreas, ovaries, and uterus, were exposed to varying levels of radiation, with the thyroid and spleen receiving particularly high doses in PTC. The study also demonstrated that the per-minute radiation exposure was consistently higher in PTC across all examined organs. The study’s findings underscore the significant radiation exposure associated with ERCP and PTC, with PTC posing a greater risk. Understanding these exposure levels is crucial for clinical decision-making, particularly when considering patients’ pre-existing conditions and sensitivity to radiation. The study highlights the need for clinicians to carefully weigh the benefits of ERCP and PTC against the potential radiological risks. It suggests a preference for ERCP in situations where radiation exposure needs to be minimized. Furthermore, the findings advocate for ongoing advancements in medical imaging techniques to reduce radiation exposure, emphasizing the importance of patient safety in fluoroscopic examinations. This research contributes significantly to informed clinical decision-making, ensuring that the selection of diagnostic and therapeutic procedures aligns with the best interest of patient health and safety.