In his first annual message, presented on December 8, 1801, Jefferson addressed the issue of immigration to the United States and what the standard for admission should be. He advocated for a liberal police on refugees. He wrote:
"Shall we refuse the unhappy fugitives from distress that hospitality which the savages of the wilderness extended to our fathers arriving in this land? Shall oppressed humanity find no asylum on this globe? The Constitution, indeed, has wisely provided that, for admission to certain offices of important trust, a residence shall be required sufficient to develop character and design. But might not the general character and capabilities of a citizen be safely communicated to every one manifesting a bona fide purpose of embarking his life and fortunes permanently with us?"
Jefferson wrote that the nation should balance its immigration policy with restrictions "to guard against the fraudulent usurpation of our flag; an abuse which brings so much embarrassment and loss on the genuine citizen, and so much danger to the nation of being involved in war". He said that "no endeavor should be spared to detect and suppress" such applicants.
In an earlier writing in his "Notes on the State of Virginia", written in 1787, Jefferson had expressed the belied that immigrants to the new nation should assimilate to the culture of their adopted homeland. He wrote: "It is for the happiness of those united in society to harmonize as much as possible in matters which they must of necessity transact together. Civil government being the sole object of forming societies, its administration must be conducted by common consent."
He elaborated his concerns on the need for assimilation of the new immigrants, stating:
"They will bring with them the principles of the governments they leave, imbibed in their early youth; or, if able to throw them off, it will be in exchange for an unbounded licentiousness, passing, as is usual, from one extreme to another. It would be a miracle were they to stop precisely at the point of temperate liberty. These principles, with their language, they will transmit to their children. In proportion to their numbers, they will share with us the legislation. They will infuse into it their spirit, warp and bias its directions, and render it a heterogeneous, incoherent, distracted mass."
Jefferson especially hoped that the new nation would attract artisans. As far as the rights afforded to new immigrants, Jefferson wrote in 1801, in a letter to Hugh White: "Born in other countries, yet believing you could be happy in this, our laws acknowledge, as they should do, your right to join us in society, conforming, as I doubt not you will do, to our established rules. That these rules shall be as equal as prudential considerations will admit, will certainly be the aim of our legislatures, general and particular."
While espousing a desire for refugees, Jefferson also recognized the need to provide balance in order to prevent too rapid an influx of immigration. In Notes on Virginia, in 1782, he wrote: "Is rapid population [growth] by as great importations of foreigners as possible founded in good policy? They will bring with them the principles of the governments they leave, imbibed in their early youth; or, if able to throw them off, it will be in exchange for an unbounded licentiousness, passing, as is usual, from one extreme to another. It would be a miracle were they to stop precisely at the point of temperate liberty. These principles, with their language, they will transmit to their children. In proportion to their number, they will share with us the legislation. They will infuse into it their spirit, warp and bias its direction, and render it a heterogeneous, incoherent, distracted mass. If they come of themselves, they are entitled to all the rights of citizenship: but I doubt the expediency of inviting them by extraordinary encouragements." He added, "I mean not that these doubts should be extended to the importation of useful artificers. The policy of that measure depends on very different considerations. Spare no expense in obtaining them. They will after a while go to the plough and the hoe; but in the meantime, they will teach us something we do not know."
He continued to have these reservations as President. In a letter he wrote in 1805, he said "A first question is, whether it is desirable for us to receive at present the dissolute and demoralized handicraftsmen of the old cities of Europe? A second and more difficult one is, when even good handicraftsmen arrive here, is it better for them to set up their trade, or go to the culture of the earth? Whether their labor in their trade is worth more than their labor on the soil, increased by the creative energies of the earth?"
In later writings, Jefferson noted a preference for those immigrants who were better able to assimilate into American culture. Writing as a retired president in 1817, he told his friend George Flower: "Although as to other foreigners it is thought better to discourage their settling together in large masses, wherein, as in our German settlements, they preserve for a long time their own languages, habits, and principles of government, and that they should distribute themselves sparsely among the natives for quicker amalgamation, yet English emigrants are without this inconvenience. They differ from us little but in their principles of government, and most of those (merchants excepted) who come here, are sufficiently disposed to adopt ours."
During Jefferson's terms in office, immigration was not as significant an issue as it would become. There was relatively little immigration to the United States from 1770 to 1830; while there was significant emigration from the U.S. to Canada, including about 75,000 Loyalists as well as Germans and others looking for better farmland in modern day Ontario. Large scale immigration would not resume until the 1830s from Britain, Ireland, Germany, and other parts of Central Europe as well as Scandinavia.
Congress passed the Naturalization Law of 1802 on April 14, 1802, during Jefferson's first term. It directed the clerk of the court to record the entry of all aliens into the United States. The clerk collected information including the applicant's name, birthplace, age, nation of allegiance, country of emigration, and place of intended settlement, and granted each applicant a certificate that could be exhibited to the court as evidence of time of arrival in the United States. This act repealed the Naturalization Act of 1798 (which had fixed a period of 14 years before certain immigrants could apply for citizenship). The act of 1802 provided that every State and Territorial court was considered a district court within the meaning of the laws pertaining to naturalization, and that any persons naturalized in such courts were accorded the same rights and privileges as if they had been naturalized in a district or circuit court of the United States. The act of 1802 was the last major piece of naturalization legislation during the 19th century.