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Significance The radical pair mechanism is the favored hypothesis for explaining biological effects of weak magnetic fields, such as animal magnetoreception and possible adverse health effects. To date, however, there is no direct experimental evidence for magnetic effects on radical pair reactions in cells, the fundamental building blocks of living systems. In this paper, using a custom-built microscope, we demonstrate that flavin-based autofluorescence in native, untreated HeLa cells is magnetic field sensitive, due to the formation and electron spin–selective recombination of spin-correlated radical pairs. This work thus provides a direct link between magnetic field effects on chemical reactions measured in solution and chemical reactions taking place in living cells.