Current plans to utilise German offshore waters as sites for windmill parks as well as ongoing investigation of potential areas to implement Natura 2000 have led to an increased research effort on local marine mammal populations. The aim of this study was to determine the spatial distribution of harbour porpoises in the German part of the North Sea and Baltic Sea. Aerial surveys were conducted from May to August 2002 using standard line-transect methodology. A total of 21 days of aerial surveying covered 8,072km tracks on effort; 4,908km were conducted in conditions of good visibility. A total of 785 harbour porpoises (488 sightings) were seen; 597 animals (427 sightings) were detected in conditions of good visibility. The study area was divided into a grid of 3 minute latitude by 6 minute longitude squares. Porpoise relative abundance and distribution were estimated as the number of animals per km on effort in each square. The results showed that in the North Sea, the highest number of porpoises per km was observed in the northeastern part of the surveyed area, close to the Danish border and in the area of Amrum Outerbank. In the Baltic Sea, the highest relative abundance of porpoises was seen in the Pomeranian Bight between the island of Rügen and the Polish border. Pod size in the Baltic was larger than in the North Sea. The aerial surveys were continued in 2003 in order to collect more information on temporal and spatial distribution of harbour porpoise and its intra and inter-annual variability in German waters. These data will serve as a baseline for management decisions.