A ship-based line transect survey was conducted in the Great Belt, Denmark, from 7-20 April 1994, covering an area of 705 linear kilometres. A total of 497 sightings were collected in sea state 0-3. A comparison of relative abundance stratified by sea state revealed that sea state had a significant effect on the estimated sighting rate, effective search width, density and abundance within sea state 0-3. However, no significant difference was found between sea state 2 and 3. Comparison of abundance estimates of the same area on two different days surveyed in sea state 0, revealed no significant difference. The relative abundance estimate was 1,526 harbour porpoises in sea state 0 within the surveyed area (326.2km2) based on the line transect method. This is the highest density of harbour porpoises (4.9 harbour porpoise/km2) reported in Europe. There is a strong indication that sea state has a significant effect on abundance estimation of harbour porpoises in ship-based conventional line transect surveys. This is important for future surveys in two ways: (1) the reliability of a comparison of abundance for different surveys strictly depends on the sea state in which the surveys were conducted; and (2) when estimating absolute abundance, effects of sea state should be explicitly addressed. One way is to separately analyse data from each sea state and apply a g(0) estimate for each sea state.