Magnetic activity indices are widely used in theoretical studies of solar-terrestrial coupling and space weather prediction. However, the indices suffer from various uncertainties, which limit their application and even mislead to incorrect conclu-sion. In this paper we analyze three most popular indices, Kp, AE and Dst. Three categories of uncertainties in magnetic indices are discussed: “data uncertainty” originating from inadequate data processing, “station uncertainty” caused by in-complete station covering, and “physical uncertainty” stemming from unclear physical mechanism. A comparison between magnetic disturbances and related indices indicate that the residual Sq will cause an uncertainty of 1―2 in K meas-urement, the uncertainty in saturated AE is as much as 50%, and the uncertainty in Dst index caused by the partial ring currents is about a half of the partial ring cur-rent. Magnetic activity indices are widely used in theoretical studies of solar-terrestrial coupling and space weather prediction. However, the indices suffer from various uncertainties, which limit their application and even mislead to incorrect conclu-sion. In this paper we analyze three most popular indices , Kp, AE and Dst. Three categories of uncertainties in magnetic indices are: “data uncertainty ” originating from inadequate data processing, “station uncertainty ” caused by in-complete station covering, and “physical uncertainty ” A comparison between magnetic disturbances and related indices indicate that the residual Sq will cause an uncertainty of 1-2 in K meas-urement, the uncertainty in saturated AE is as much as 50%, and the uncertainty in Dst index caused by the partial ring currents is about a half of the partial ring cur-rent.