There is a worldwide increase in macrolide-resistant Mycoplasma genitalium strains, with severe impacts on treatment. The aim of this study was to compare three real-time PCR methods for the detection of macrolide resistance: an in-house PCR described by Touati et al., ResistancePlus® MG (SpeeDx), and S-DiaMGRes™ (Diagenode Diagnostics). One hundred M. genitalium-positive patient samples collected in Sweden and a quantitated M. genitalium DNA control were analyzed. Macrolide resistance was detected in 18, 15, and 16 of the samples with the respective methods. Sequencing of the 23S rRNA gene confirmed resistance in 16 (16%) of 100 samples in which it was detected with any of the three methods. ResistancePlus® MG and S-DiaMGRes™ falsely determined one sample as macrolide-sensitive, but this sample was determined as resistant when retested. The sensitivity of the methods was comparable, although there should be awareness of possible incorrect determination of macrolide resistance, especially of low-positive samples.