Objective: The correct estimation of the portosystemic shunt (PSS) ratio prior to surgery for patent ductus venosus is important. Until now, formulas using the lung and liver uptake for per-rectal portal scintigraphy using 123I-iodoamphetamine (IMP) have been mainly used for calculating the PSS ratio. However, these methods did not take radioactivity in the brain or changes in organ radioactivity over time into consideration. Here, we performed sequential whole-body scanning by per-sigmoid colon 123I-IMP scintigraphy, and evaluated the changes in radioactivity in the liver, lungs, and brain over time. Methods: The patient was 7-year-old boy with a patent ductus venosus. A 10 Fr. catheter was inserted into the sigmoid colon under fluoroscopic guidance, through which about 55.5 MBq of 123I-IMP was administered. Following the administration, the patient was placed in the supine position and sequential whole-body scanning (from head to thigh) was performed for up to about 80 min. Four regions of interest (ROIs) were placed on the whole brain, lungs, liver, and mediastinum. The PSS ratios were calculated using both the traditional formula (PSS index: brain uptake is not considered) and our original formula (new index: brain uptake is considered). Results: Prior to surgery, the radioactivity could be seen clearly in the brain and lungs just following the injection. The liver uptake was faint on the first and second scans (15 min/scan), and increased gradually over time. In contrast, almost no radioactivity was detected in the brain or lungs following surgery. The liver uptake could be seen clearly just following the injection. The new index was significantly higher than the PSS index. Both the new index and the PSS index showed changes over time especially prior to surgery. Conclusions: Distinct brain radioactivity was observed early following administration in a patient with PSS. The calculation of the PSS fraction should be performed taking the brain radioactivity into consideration. The timing of the scan should be fixed, but 30 min following administration may be too early to begin scanning.