In 1798, during the quasi-war with France, the Federalist-controlled Congress passed the "Alien Acts," part of which changed the residency requirement to become a naturalized citizen from five to fourteen years. Jefferson and the Democratic Republicans recognized this change in the law effectively denied citizenship to recent immigrants escaping conflict in Europe. This issue, along with the Sedition Acts, which effectively made it illegal to criticize President Adams or the Congress, became significant factors in the election of 1800. When Jefferson defeated Adams, the Naturalization Act of 1802 changed the residency requirement back to five years.

In Jefferson's own words:

"I can not omit recommending a revisal of the laws on the subject of naturalization. Considering the ordinary chances of human life, a denial of citizenship under a residence of 14 years is a denial to a great proportion of those who ask it, and controls a policy pursued from their 1st settlement by many of these States, and still believed of consequence to their prosperity; and shall we refuse to 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 everyone manifesting a bona fide purpose of embarking his life and fortunes permanently with us, with restrictions, perhaps, 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 that no endeavor should be spared to detect and suppress it?"
- Thomas Jefferson, 1802