C11-BODIPY(581/591) is a fluorescent lipid peroxidation reporter molecule that shifts its fluorescence from red to green when challenged with oxidizing agents, i.e., reactive oxygen species (ROS) or reactive nitrogen species (RNS). To understand the molecular mechanism responsible for this shift, we studied the molecular rearrangements leading to the shift in fluorescence in C11-BODIPY(581/591). Furthermore, we aimed to determine if these rearrangements were dependent on the nature of the applied ROS, in homogenous solution, bilayer vesicles, and living cells. C11-BODIPY(581/591) was challenged with various ROS- or RNS-generating systems, including peroxynitrite, NO(2)(?), peroxides, and hydroxyl, alkoxyl, tyrosyl, and peroxyl radicals. The reaction products were subsequently analyzed by means of mass spectrometry. Our results show that the initial target for free radical-mediated oxidation is the conjugated diene interconnection between the BODIPY core and the terminal phenyl moiety, which already explains the shift in fluorescence properties of the probe. After oxidative challenge, three different stable products were identified, one of which was specific for oxidation by peroxynitrite. The two other stable end products had lost the entire phenyl moiety, irrespective of the type of radical generating system used. These products were also recovered from Rat-1 fibroblasts stressed either by GSH depletion/serum starvation or by exposure to peroxynitrite, and were the only C11-BODIPY(581/591) oxidation products detectable in these cells.