1. High-resolution fishing effort data from the Kattegat, an important fishing ground for Swedish and Danish fishermen, was analysed in a Geographical Information System (GIS). Data were based on position data for individual tows reported by Swedish fishermen during 2001-2003. 2. Gear dimension and towing speed data were used to calculate an index for area swept per hour for each main gear type in use in the area. These indexes were multiplied by fishing effort and a grid theme of fishing intensity was created after GIS analysis. 3. Around 44% of the entire area was affected by Swedish fisheries during the study period, hence 56% was not affected. 4. Effort was highly concentrated in certain areas and 10% of the total area was covered more than twice per year. 5. Overlaying the effort data set with habitat maps classified according to the European Nature Information System (EUNIS) showed that the fishing pressure differed between habitats. For deep rocky and muddy habitats, almost the entire area was affected by fisheries during the study period, while both intensity and proportion affected were lower in sandy sediments and gravels. 6. Around 55% of the deep rocky habitats were trawled more than twice per year. Of the muddy seafloor areas, 41% were covered more than twice per year and 4% more than once a month by trawls. 7. The biological effects of the fishing intensities found were analysed using a database (MarLIN) containing assessments of marine habitat recoverability. All habitats except muds are probably in a nearly or fully recovered condition (as defined by MarLIN). A considerable part of the muddy habitats are in a permanently altered condition owing to fishing disturbance taking place more frequently than the indicated recovery time. 8. Danish fishermen report more fishing effort in the area than do Swedes. Owing to differences in reporting fishing positions, Danish fisheries could not be included in the present study. Scaling up the results to include Danish fisheries is discussed. 9. The results of the present study could be used to target habitat management goals more precisely, while minimizing the negative impact of restrictions on the fishing sector. 10. A prerequisite for performing similar studies is the availability of high-resolution fishing effort data and high-resolution benthic habitat maps. Copyright © 2006 John Wiley & Sons, Ltd.