Although it is well known that plants emit ultrasound bursts under drought stress, the exact origin of the acoustic waveform of these pulses has remained elusive. Here we present evidence for a correlation between the ultrasound spectrum of these pulses and the dimensions of the plant’s xylem vessels. Using a model that relates the vibrational excitations of the vessels to their geometric and viscoelastic properties, we develop a methodology to extract the internal xylem vessel dimensions from recorded ultrasound waveforms. We apply the method to ultrasound pulses from drying shoots of three vascular dicot plant species, and validate it by comparison with destructive measurements via microscopy. Our method demonstrates the potential for continuous monitoring of the vascular anatomy of plants. The ultrasonic, non-invasive characterization of internal vessel dimensions can lead to breakthroughs in speed and accuracy in plant phenotyping and disease detection in agriculture.