Z-spectrum imaging (ZSI) was used to characterize brown adipose tissue (BAT) features in polycystic ovary syndrome (PCOS) patients compared to healthy subjects. Fat-water fraction (FWF) was derived from the fitting of the direct saturation of water and fat in ZSI. BAT segmentation allowed the measurement of BAT-specific FWF and area. PCOS group showed increased FWF and reduced BAT area compared to controls, likely due to reduced BAT cells activity and lipid accumulation. ZSI can therefore be used to study BAT characteristics in vivo in metabolic disorders.