An animal’s body condition directly influences its survival and reproductive fitness, and therefore also the health of the populations. Monitoring cetaceans’ morphometric measurements are usually obtained from stranded or bycaught individuals. This may bias interpretations on age-and sex-related growth as well as the status of their populations. The purpose of this study was to determine morphometric measurements of harbour porpoises (Phocoena phocoena) by using overhead video recordings from commercial UAVs (Unmanned Aerial Vehicles). From a customised program that implements the UAV parameters (height, gimbal orientation, camera parameters and Field of View), we were able to obtain the length and girth of 7 individual harbour porpoises of known sizes, very similar to the actual measurements and with a maximum error of 7.4%. Using length and girth, enabled determination of a body condition score (BMI Index) for each animal with an overall average error of 0.8 points. The method was then applied on recordings of free-ranging harbour porpoises with calves to determine the body condition. Furthermore the length was used to predict an approximate age, that all corresponded with the calves being born during spring. This is a very cost-effective monitoring method and a valuable complement to the current body assessment methods from bycaught or stranded animals that can aid in monitoring the growth and health of calves and adults on population scales throughout various seasons.