The study’s purpose was to assess the performance of Self-gated Non–Contrast-Enhanced Functional Lung (SENCEFUL)-MRI in detecting pulmonary perfusion deficits in patients with cystic fibrosis (CF). Nineteen patients with cystic fibrosis and 19 matched healthy controls underwent SENCEFUL-MRI at 1.5T. Four blinded readers rated perfusion and phase (i.e. temporal distribution of pulmonary blood flow) maps separately regarding local deficits followed by simultaneous assessment of both maps. Furthermore, phase data was plotted in histograms for objective comparison to the reader’s results. SENCEFUL-MRI revealed statistically significant differences between CF-patients and controls. Furthermore, it demonstrated its potential in detection of pulmonary perfusion deficits.