Both the nationality and ethnicity of Copernicus are disputed. His father has been described as a Pole, and his mother was most likely of German origin. The family came originally from the Silesian village of the same name (Coprnik, Copernik, Copirnik, Copernic, Kopernic, today Koperniki) near Nysa. In the 14th century, members of the family had begun moving to Silesian and later to Polish cities: Kraków (1367) and Toruń (1400), and also to Lviv (1439 - then the Polish city, Lwów). The astronomer's father (probably the son of Jan) came from the Kraków line. He appears in records for the first time in 1448 as a well-to-do merchant who dealt in copper with Gdańsk. In the early period of the Pomeranian cities' struggle for independence from the Teutonic Order, in August 1454, he mediated financial negotiations between Cardinal Zbigniew Oleśnicki and the great Prussian cities regarding repayment of a loan for the Polish-Teutonic war. About 1458 the future astronomer's father moved from Poland's capital, Kraków, to Toruń, where a few years later (before 1464) he married Barbara, daughter of a wealthy Toruń patrician and city councilor, Lucas Watzenrode the elder.

The Watzenrodes had likewise come from Silesia, from the Świdnica (Schwednitz) region, and had settled in Toruń after 1360. The astronomer's grandfather Watzenrode was a decided opponent of the Teutonic Order. In 1453 he was the delegate from Toruń at the Grudziądz conference that planned the anti-Teutonic-Order uprising, and during the Thirteen Years' War he actively supported the struggle of the Prussian cities not only with substantial monetary subsidies but with political activity in Toruń and Gdańsk as well as with his own personal participation in battles at Łaszyn and Malbork. He died in 1462, leaving three children: Lucas (1447–1512), future Bishop of Warmia and the astronomer's patron, and two daughters: Barbara, the astronomer's mother (died after 1495), and Christina (died before 1502), who in 1459 married the merchant and Toruń mayor, Tiedeman von Allen. Through the Watzenrodes' extensive family relationships by marriage, the future astronomer was related both to wealthy burgher families of Kraków, Toruń, Gdańsk and Elbląg and to prominent noble families of Prussia: the Działyński, Kościelicki and Konopacki families.

It has been suggested that Copernicus's "mother tongue" was German. While he was fluent in German and communicated with many German scholars, no direct evidence survives of the extent of his knowledge of Polish. Typically for the time, his main language for written communication was Latin. It remains a matter of dispute whether a "nationality" should be ascribed to Nicolaus Copernicus retrospectively and, if so, whether he should be considered German or Polish. Nevertheless, the 1875 Allgemeine Deutsche Biographie acknowledged the Polish aspects of Copernicus' life. Current German sources call the controversy, as reflected in the older literature, superfluous and shameful. Encyclopædia Britannica, Encyclopedia Americana, and the Microsoft Encarta Online Encyclopedia identify Copernicus as Polish.

Copernicus was born, grew up, and spent most of his life in Royal Prussia and therefore was a subject of the Crown of the Polish Kingdom. This is a principal reason why he is generally regarded as Polish. The fact that Copernicus oversaw the defense of Olsztyn Castle at the head of Royal Polish forces when the town was besieged by the Teutonic Knights is used by some to support the claim that his bond with the Kingdom of Poland was much stronger than his German ties. On the other hand, the urban elites of Royal Prussia comprised German-speaking burghers who had only lately revolted against the Teutonic State with the aid of the Polish Kingdom. It is unlikely that in the short space of 20 years they had been 'Polonized' in any substantial way, at least in the modern sense of the term. It is no doubt that he was a loyal citizen of the Polish Crown.

Nevertheless, some have preferred to assign a single nationality to Copernicus. In 1807, a bust of Copernicus was one of the first busts to be prepared for enshrinement at the Walhalla temple, the German hall of fame built by King Ludwig I of Bavaria. Later, Nazi Germany claimed Copernicus to have been purely German. After 1945, German public opinion returned to a more balanced view. Some Soviet-bloc-era publications in socialist East Germany pronounced Copernicus a Pole.

In Poland, in 1973, the 500th anniversary of Copernicus' birth saw celebrations of a "great Pole". Poland issued a banknote bearing Copernicus' portrait. Thirty years later, on June 12, 2003, the Polish Senate pronounced Copernicus an "exceptional Pole."