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While researching genealogy, I discovered that one of my ancestors had a "Registration Affidavit of Alien Enemy" document on file. It is dated 1 January 1918 and includes his fingerprints, immigration information (he was a German immigrant), and living situation.

I'm aware that there was anti-German prejudice at the time in the United States, which is why he is labeled as an "alien enemy". But I'm unsure as to what this document actually means.

Is it merely stating that he's a German immigrant, without otherwise commenting on him? Is it saying that he was specifically identified as an individual who was hostile to Americans, perhaps through his speech or actions? Was he under individual suspicion for being a German sympathizer?

What does this "Registration Affidavit of Alien Enemy" document actually mean?

Short answer

This was a requirement for all "natives, citizens, denizens, or subjects" of the German (and, a few months later, the Austro-Hungarian) Empire; thus, 'alien enemy' registration was not about targeting individuals and - for the vast majority - did not lead to internment. It did mean, though, that thousands of people's lives were adversely affected in one or more ways.

For those interned, most were put in camps because of suspected 'disloyal behaviour' or being 'involved in radical politics or labour unrest'.

Details

Registration was required for

all males in the United States older than 14 who
were "natives, citizens, denizens, or subjects" of the German Empire
were required to register as alien enemies. In 1918, an act of
Congress included women aged 14 and older.

In more detail,

After America entered the war on 6 April 1917, German nationals were
subject to a series of restrictions on their lives, property and
freedom of movement imposed by President Woodrow Wilson (1856-1924)
under the 1798 Alien Enemy Act, including bans on entering "forbidden
zones", compulsory registration with the police or U.S. postmasters,
prohibition on owning signalling apparatus, radios and firearms, and
so on. At various points these restrictions were increased or
exemptions revoked, largely to appease public opinion. They were also
extended to Austro-Hungarians in December 1917 and to all female enemy
aliens in April 1918.

'Alien enemies' had to have a registration card on them at all times and permission was needed to travel or change residence. Restrictions were ended on 25th December, 1918, some six weeks after the armistice.

This requirement was deemed necessary because

government officials believed these denizens to be the most probable
spies and saboteurs, they felt it necessary to classify and monitor
these individuals.

Failure to register could have severe consequences:

The Minnesota Commission of Public Safety laid out strict consequences
for all delinquents: "Any alien resident of the State of Minnesota who
fails to register and make prescribed declaration on one of the above
designated registration days will be interned or subjected to other
action which the Minnesota Commission of Public Safety will
prescribe."

For failing to register,

Internment could last for an unspecified period of time, or until the
end of the war.

Nonetheless, many Germans delayed registering so long that the deadline for registration in Minnesota had to be extended by two due to a deluge of applicants on the (original) deadline day.

It appears that some states went beyond the restrictions mandated by the Federal government:

Several Midwestern states which had previously granted suffrage to
aliens holding first naturalization papers rescinded these laws.
Aliens were also expelled from all ships and boats except public
ferries, as well as anything deemed to have military importance, from
wharves to railroad depots.

while in Wisconsin posters were put up telling aliens "Work or Go to Jail", the penalty for 'listlessness' being 3 months in jail.

In general,

Violations were dealt with harshly, and police round-ups became
common. Surveillance operations indeed led to over 10,000 arrests,
8,500 of which were conducted under presidential warrants, the rest
carried out by local justice officials who then reported their actions
to the Justice Department in Washington D.C. Most were paroled after a
short period of "investigation" into their circumstances, although the
arrest itself was a humiliating experience and could lead to loss of
employment, social standing, housing or all three.

In California, though, two brothers who failed to register were not interred, even though one of them was 'caught' in a restricted area so there was (perhaps not surprisingly) some inconsistency).

For those who were interned,

Around 10 percent of the 2,300 civilian internees held at Fort
Oglethorpe and Fort Douglas were wealthy German-born immigrants
suspected of disloyal behaviour, including financing pro-German
propaganda. A much bigger contingent was made up of ordinary workers,
however, including the destitute and unemployed, and many whose only
"crime" was to have been involved in radical politics or labour
unrest.... However, even in the case of anti-war agitators, the
American authorities were still inclined to investigate each
individual case rather than making blanket referrals for internment.

tl; dr

The fact that your ancestor has a "Registration Affidavit of Alien Enemy" document on file doesn't mean that they had actually done anything wrong. All German immigrants who weren't naturalised US citizens had to complete the registration.

If there had been suspicion that he was a German sympathiser he might also have been interned for the duration of the war (some 2,048 individuals were actually incarcerated at two internment camps).

Guide to the Registration of German alien enemies

There was a guide to the Registration of German alien enemies produced by the US Department of Justice in 1918. It contains a wealth of information about the process your ancestor would have had to go through.

In the preamble, or 'General Regulations', dated 31 December 1917, the guide explains the background:

Whenever there is declared a war between the United States and any foreign nation op government, or any invasion or predatory incursion is perpetrated, attempted, or threatened against the territory of the United States, by any foreign nation or government, and the President makes public proclamation of the event, all natives, citizens, denizens, or subjects of the hostile nation or government, being males of the age of fourteen years and upward, who shall be within the United States and not actually naturalized, shall be liable to be apprehended, restrained, secured, and removed as alien enemies.

For the specific case of the First World War, Article I explained who was required to register:

All natives, citizens, denizens or subjects of the German Empire or of the Imperial German Government, being males of the age of 14 years and upward, who are within the United States and not actually naturalized as American citizens, are required to register as alien enemies.

Article II then went into greater detail about "Definitions to be observed in the interpretation, construction and enforcement of these regulations".

The Registration Form

Article VII included a copy of the form that was to be completed (all the information that most genealogists could want!):

(click to enlarge)

After your ancestor had registered, he would have been issued a Registration Card, the details of which are provided by Article IX.

Impact of registration

For most people, registration had no significant effect beyond being required to carry their registration card at all times. A relatively small number were identified as being a risk to national security, and interned for the rest of the war. The Wikipedia page on the Internment of German Americans notes:

Some 250,000 people in that category were required to register at their local post office, to carry their registration card at all times, and to report any change of address or employment. (...) Some 6,300 such aliens were arrested. Thousands were interrogated and investigated. A total of 2,048 were incarcerated for the remainder of the war in two camps, Fort Douglas, Utah, for those west of the Mississippi, and Fort Oglethorpe, Georgia, for those east of the Mississippi

Surviving records

Unfortunately, many of these records were lost or destroyed, so you are quite fortunate to ave found a copy. More generally, the records that do survive are held at one of the regional branches of the US National Archives.