In this paper, we report the development of the first high-frequency (HF) pulsed-wave Doppler system using a 30-MHz linear array transducer to assess the cardiovascular functions in small animals. This array-based pulsed-wave Doppler system included a 16-channel HF analog beamformer, a HF pulsed-wave Doppler module, timing circuits, HF bipolar pulsers and analog front ends. The beamformed echoes acquired by the 16-channel analog beamformer were fed directly to the HF pulsed-wave Doppler module. Then the in-phase and quadrature-phase (IQ) audio Doppler signals were digitized by either a sound card or a Gage digitizer and stored in a personal computer. The Doppler spectrogram was displayed on a personal computer in real time. The two-way beamwidths were determined to be 160 microm to 320 microm when the array was electronically focused at different focal points at depths from 5 to 10 mm. A micro-flow phantom, consisting of a polyimide tube with an inner diameter of 127 microm and the wire phantom were used to evaluate and calibrate the system. The results show that the system is capable of detecting motion velocity of the wire phantom as low as 0.1 mm/s, and detecting blood-mimicking flow velocity in the 127-microm tube lower than 7 mm/s. The system was subsequently used to measure the blood flow in vivo in two mouse abdominal superficial vessels, with diameters of approximately 200 microm, and a mouse aorta close to the heart. These results demonstrated that this system may become an indispensable part of the current HF array-based imaging systems for small animal studies.