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During the second half of the 18th century, Aalborg entered a further period of prosperity.

In Erik Pontoppidan's Danske Atlas (Danish Atlas) it was described as "after Copenhagen, the best and most prosperous market town in Denmark".

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The herring fishery linked Aalborg to the East coast of England, across the North Sea, both in commercial competition and cultural exchange.

During the Middle Ages a number of important institutions were established in Aalborg, including Budolfi Cathedral in the late 14th century and the Hospital of the Holy Ghost, a monastery and nunnery founded in 1451 to help those in need.

1040, the period when King Harthacnut (Hardeknud) settled in the area. 1075, Adam of Bremen reported that Alaburg, as he called it in German, was an important harbour for ships sailing to Norway.

Grey Friar Convent, on the east side of Østerå, was probably built around 1240; it was documented in 1268 when it was a Franciscan Convent of the Order of Friars Minor, but like many other Roman Catholic monasteries and convents was shut down in 1530 as a result of the Reformation.

The town prospered, becoming one of the largest communities in Denmark.

Its prosperity increased when the merchant- and trade association Guds Legems Laug was established in 1481, facilitating trade with the Hanseatic League, The king frequently visited the town, where he held court and stayed in the old Aalborghus.In 1530 a large part of the town was destroyed by fire, and in December 1534 it was stormed and plundered by the king's troops after a peasants' revolt known as the Count's Feud led by Skipper Clement. From the 1550s to the 1640s, as a result of increased foreign trade, Aalborg enjoyed great prosperity, second only to that of Copenhagen.The population grew in parallel with the development of many fine buildings in the city as merchants benefitted from their shipping routes from Norway to Portugal.Aalborg's earliest trading privileges date from 1342, when King Valdemar IV received the town as part of his huge dowry on marrying Helvig of Schleswig.The privileges were extended by Eric of Pomerania in 1430 and by Christopher of Bavaria in 1441.By road Aalborg is 64 kilometres (40 mi) southwest of Frederikshavn, and 118 kilometres (73 mi) north of Aarhus.