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Per rectal portal scintigraphy using 99mTechnetium pertechnetate (99mTcO4-) was used to diagnose portosystemic shunts (PSS) before surgical confirmation in seven dogs and two cats. Shunt fractions, representing the percent of portal blood that bypasses the liver, were determined by computer analysis of the scintigraphic images. Animals with portosystemic shunts had a mean preoperative shunt fraction of 84.02% (n = 9). The mean postoperative shunt fraction in four animals was 58.22%. The mean shunt fraction in ten control dogs was 5.00%. Per rectal portal scintigraphy is an innovative, easily performed, inexpensive method to diagnose congenital portosystemic shunts in dogs and cats.