A mobile and fast, semi-automatic ultrasound (US) system was developed for facial soft tissue depth registration. The system consists of an A-Scan ultrasound device connected to a portable PC with interfacing and controlling software. For 52 cephalometric landmarks, the system was tested for repeatability and accuracy by evaluating intra-observer agreement and comparing ultrasound and CT-scan results on 12 subjects planned for craniofacial surgery, respectively. A paired t-test evaluating repeatability of the ultrasound measurements showed 5.7% (n = 3) of the landmarks being significantly different (p < 0.01). US and CT-scan results showed significant differences (p < 0.01) using a Wilcoxon signed rank test analysis for 11.5% (n = 6) of the landmarks. This is attributed to a difference in the volunteer's head position between lying (CT) and sitting (US). Based on these tests, we conclude that the proposed registration system and measurement protocol allows relatively fast (52 landmarks/20 min), non-invasive, repeatable and accurate acquisition of facial soft tissue depth measurements.