Dioxins and PCBs are toxic, lipophilic, and persistent substances that impose a serious health threat. A major risk of exposure to these toxic substances is consumption of fish from polluted waters, such as the Baltic Sea. The aim of this study was to investigate if pH-shift processing of Baltic herring with elevated toxicity levels could be used to produce a protein isolate with low fat content and, thereby, reduced dioxin and PCB levels. Both acid (pH 2.7) and alkaline (pH 11.2) pH-shift processing were investigated and resulted in efficient reduction of fat, dioxin, and PCB levels. A reduction of 70-80% per amount of protein was determined for all of these parameters. The amounts, and thus the removal, of lipids and dioxins (R(2) = 0.952) as well as lipids and PCBs (R(2) = 0.996) were highly correlated (p < 0.01). A mass balance of the alkaline pH-shift process showed that most of the fat and pollutants were found in the floating fat emulsion layer of the first centrifugation, followed by the pellet of the first centrifugation. These data show that the pH-shift protein isolation technique can be used to process herring with elevated dioxin and PCB levels and thereby increase the usage possibilities of such fish.