The motion of ships can cause discomfort and stress in humans, but little is known about the impact on sheep welfare, despite many sheep traveling long distances by ship during live export. We tested whether exposing sheep to roll (side to side movement), heave (up and down movement), and pitch (front to back movement) with similar amplitude and period conditions to a commercial livestock transport vessel would affect their behavior and physiology. Specifically, we tested the effects of these motions and a control treatment on behavior, heart rate variability, rumination, body posture, and balance of sheep. Four sheep (37 ± 0.1 kg) were restrained in pairs in a crate, which was placed on a moveable and programmable platform that generated roll and pitch motions. An electric forklift was used to produce heave motion. The treatments were applied for 30 min each time in a changeover design with 1 repetition over 8 consecutive days. Sheep behavior was recorded continuously from video records, and heart rate monitors were attached to determine heart rate and its variability. Heave reduced the time that sheep spent ruminating, compared with the other 3 treatments ( < 0.001). The 2 sheep spent more time during heave with their heads 1 above the head of the other ( < 0.001) and looking toward their companion ( = 0.02), indicating greater affiliative behavior. Sheep spent more time during heave standing with their back supported on the crate ( = 0.006) and less time lying down ( = 0.01). Roll caused more stepping motions than pitch and control, indicating loss of balance ( < 0.001). Sheep experiencing heave and roll had increased heart rates and reduced interbeat intervals (IBI) compared to the control ( < 0.001). The IBI of sheep in the heave treatment had an increased ratio of low to high frequency duration ( = 0.01), indicating reduced parasympathetic control of stress responses. Therefore, there was both behavioral and physiological evidence that heave and roll caused stress, with sheep experiencing roll apparently coping better by regular posture changes and heave causing the sheep to seek the close presence of their companion.