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In this paper we analyze the contribution of different sources of noise to the total output noise of a magnetometer based on fundamental mode orthogonal fluxgate. We show that the main contribution to the noise is not given by noise generated in the electronics nor due to the noise of the excitation current in the wire. In fact, a large part of the noise has magnetic origin and it is generated within the core. Therefore, any attempt to reduce the noise of the magnetometer should be focused on the core at a first stage. We give a model, which describes the behavior of both 1/f noise and noise floor as a function of several variables affecting the working mode of the sensor. This model can be used to optimize the parameters of the magnetometer in order to achieve the lowest possible noise. This model can be also useful as a reference to move toward a further reduction of the noise by developing a sensor with better parameters.