In this paper, the input/output transfer functions involved in a selective filtering using shunt active filters are analyzed. Their dependence on the employed control method for harmonic current filtering is studied. When performing selective filtering of harmonic sequences, the I/O transfer functions may have non-real terms. For those cases, a suitable frequency-domain analysis method, which takes into account both positive and negative current sequence filtering, is presented. The calculation procedure for the active filter reference current is then analyzed. The series and parallel calculation methods are presented and compared. The advantages of each method depending on the use of load or line current control are shown. The interference between the different filtering blocks obtained by using both series and parallel calculation methods is also shown.