Located in Northern Europe, Denmark consists of the peninsula of Jutland and 443 named islands (1,419 islands above 100 square metres (1,100 sq ft) in total). Of these, 72 are inhabited, with the largest being Zealand and Funen. The island of Bornholm is located east of the rest of the country, in the Baltic Sea. Many of the larger islands are connected by bridges; the Øresund Bridge connects Zealand with Sweden; the Great Belt Bridge connects Funen with Zealand; and the Little Belt Bridge connects Jutland with Funen. Ferries or small aircraft connect to the smaller islands. The largest cities with populations over 100,000 are the capital Copenhagen on Zealand; Aarhus and Aalborg in Jutland; and Odense on Funen.

Denmark occupies an area of 43,094 square kilometres (16,638.69 sq mi). The size of the land area of Denmark cannot be stated exactly since the ocean constantly erodes and adds material to the coastline, and because of human land reclamation projects (to counter erosion). It shares a border of 68 kilometres (42 mi) with Germany to the south and is otherwise surrounded by 7,314 km (4,545 mi) of tidal shoreline (including small bays and inlets). No location in Denmark is further from the coast than 52 km (32 mi). On the south-west coast of Jutland, the tide is between 1 and 2 m (3.28 and 6.56 ft), and the tideline moves outward and inward on a 10 km (6.2 mi) stretch.

Denmark's northernmost point is Skagen's point (the north beach of the Skaw) at 57° 45' 7" northern latitude; the southernmost is Gedser point (the southern tip of Falster) at 54° 33' 35" northern latitude; the westernmost point is Blåvandshuk at 8° 4' 22" eastern longitude; and the easternmost point is Østerskær at 15° 11' 55" eastern longitude. This is in the archipelago Ertholmene 18 kilometres (11 mi) north-east of Bornholm. The distance from east to west is 452 kilometres (281 mi), from north to south 368 kilometres (229 mi).

The country is flat with little elevation; having an average height above sea level of 31 metres (102 ft). The highest natural point is Møllehøj, at 170.86 metres (560.56 ft). The area of inland water is 700 km² (270 sq mi).

Phytogeographically, the Kingdom of Denmark (including Greenland and the Faroe Islands) belongs to the Boreal Kingdom and is shared between the Arctic, Atlantic European, and Central European provinces of the Circumboreal Region. According to the World Wide Fund for Nature, the territory of metropolitan Denmark can be subdivided into two ecoregions: the Atlantic mixed forests and Baltic mixed forests. The Faroe Islands are covered by the Faroe Islands boreal grasslands, while Greenland hosts the ecoregions of Kalaallit Nunaat high arctic tundra and Kalaallit Nunaat low arctic tundra.