Quantitative magnetic resonance (MR) images of flow velocities in intact corn plants were acquired using magnetization-prepared MR microscopy. A phase contrast flow imaging technique was used to quantitate water flow velocities and total volume flow rates in small xylem vessels. The simultaneous measurement of the transpiration of the whole plant was achieved by using a closed climate chamber within the MR magnet. The total volume flow rate and the transpiration values were in close correlation. Functional magnetic resonance imaging in intact plants was performed by light stimulation of the transpiration inside of the magnet. The change in the flow velocities in the xylem vessels of single vascular bundles was in correlation with the changes in the transpiration. Significant differences were observed between the xylem vessels in different vascular bundles. Furthermore, flow velocity measurements were performed on excised plant stems and visualized by the uptake of the MR contrast agent, gadolinium-diethylenetriamine pentaacetic acid (Gd-DTPA). A comparison between the phase contrast flow imaging and the contrast media uptake showed to be in good agreement with each other.