Electromagnetic interference (EMI) generated by renewable generation systems in the grid receives increased attention especially in the low frequency range, given the typical switching frequencies of high-power inverters. It is therefore very important to be able to derive EMI models of power inverters as well as develop strategies to reduce the related conducted emissions. This study applies black-box modeling to a three-phase inverter system, by implementing an alternative procedure to identify the parameters that describe the active part of the model. It also examines two limitations of black-box modeling. The first is the need for the system to satisfy the assumption of linearity and time-invariance (LTI). The influence of this hypothesis on the prediction accuracy is analyzed by referring to the decomposition into zero, positive and negative sequences. It is shown that the predictions for the positive/negative sequences are strongly influenced by this hypothesis, unlike those for the zero sequence. The second limitation is the possible variation of the network impedance which is not stabilized satisfactorily at low frequencies since it is outside the operating frequency range envisaged by the regulations for line impedance stabilization networks.