A method and apparatus is disclosed for MR perfusion acquisition using a notched RF saturation pulse. In acquiring such MR data, a volume of slice locations is selected in which MR data is to be acquired. Each given slice is prepared with a notched RF saturation pulse which has a stop-band between a pair of pass-bands. The stop-band is designed to not affect the spins in the next slice in which MR data is to be acquired thereby effectively increasing the TI and increasing SNR and contrast simultaneously. Since the notched saturation pulse saturates all the spins outside of the notched stop-band, the blood in the ventricular chamber is effectively saturated so that the resulting perfusion images have blood pool suppression. Additionally, the use of a 90° presaturation RF pulse provides a high level of immunity to the effects of arrhythmias or other variations in the patient's heart rate. In order to keep the stop-band, or the notch, as wide as possible to overlap the boundaries of each slice location, it is preferable to interleave the acquisition of slice locations.