The objective was to assess the optimal procedure for real-time, three-dimensional (3D) ultrasound (US) imaging for assessing the equine fetus during the first half of gestation and the possibility of using 3D US imaging of the equine fetus in clinical applications. Seventeen pregnant mares were examined by 3D US between Days 35 and 180 of gestation. Abdominal and endo-vaginal real-time 3D transducers used in human medicine were used for transrectal and transvaginal examinations, respectively. Images were recorded by both 3D stationary and real-time movies. In a comparison of four methods, transrectal examination with a bulb-shaped abdominal 3D transducer enabled the equine fetus to be clearly visualized, and did not require sedation of the mare. Therefore, this approach was the most suitable procedure for examining equine fetuses during the first half of gestation. Each scan required only a few seconds and an entire examination took <10 min in total. The 3D volume image was easy to restore after the examination and could be rotated to any angle the examiner desired. Fetal surface structures, including the head, body, limbs, and genital tubercle, were observed as 3D images which enabled fetal development to be characterized. For early (Days 60–70), but not later (Days 90–150) periods, 3D ultrasonography was not able to evaluate fetal structure in detail as well as conventional 2D ultrasonography. In conclusion, 3D ultrasonography of the equine fetus was a valuable adjunct to 2D ultrasonography and a convenient modality for more detailed assessment of fetal structures.