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I was reading an article about the citizenship question on the decennial US census. The article said that including the citizenship question would discourage immigrants from participation in the census. Among other points, it claimed that this would lead to an undercount which would skew representation in Congress.

My first thought is that only citizens are counted for representation, but maybe that's wrong. So who is counted for representation in the US Congress? Has it always been that way and if not, how has it changed?

Everyone who resides in the 50 states of the United States is counted, including noncitizens. U.S. Armed Forces personnel and federal civilian employees stationed outside the United States are also counted.

From the US Census Bureau website:

Who is included in the apportionment population counts?

The apportionment calculation is based upon the total resident population (citizens and non-citizens) of the 50 states. In the 2010 Census, the apportionment population also includes U.S. Armed Forces personnel and federal civilian employees stationed outside the United States (and their dependents living with them) that can be allocated, based on administrative records, back to a home state. This is the same procedure used in 2000.

(emphasis mine)

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Are undocumented residents (aliens) in the 50 states included in the apportionment population counts?

Yes, all people (citizens and noncitizens) with a usual residence in the 50 states are to be included in the census and thus in the apportionment counts.

According to this Congressional Research Service report, noncitizens have always been counted in previous censuses.

In the 2010 decennial census, the Census Bureau counted the total population of the United States. This included, as in previous censuses, all U.S. citizens, lawfully present aliens, and unauthorized aliens.

[ ... ]

Some have pointed to the fact that the census has historically included questions about citizenship, thus perhaps suggesting that a distinction has been made between citizens and aliens for purposes of counting individuals. It is true that at least two early censuses (1820 and 1830) included a category for foreigners not naturalized and later censuses asked about place of birth. However, such information was not used to exclude any aliens from the census count. Rather, it is clear that such individuals were included in the total count, and it appears the data were collected for informational purposes (similar to how information was collected about age, occupation, etc). It does not appear that aliens have been excluded from any census.

(emphasis mine)

However, before the Fourteenth Amendment was adopted, slaves were counted as three-fifths of a person, per Article I Section 3 of the Constitution. (More details in @Brythan’s answer.)

So who is counted for representation in the US Congress? Has it always been that way and if not, how has it changed?

The three-fifths compromise in the United States constitution (Article I, Section 2, paragraph 3) involved counting slaves (obviously not citizens much less voters) at three-fifths of a free person. This dates back to the founding, so it has always been that way. Children and women were counted even though they couldn't vote. So a district with many large families would effectively give male voters more political power than one with smaller families. And of course slave states had relatively more influential (measured by voters per representative; lower is better) voters than free states.

There was a Supreme Court case recently that argued that non-citizens should not count, Evenwell v. Abbott. The court ruled that states could continue to use total population to balance district size. It did not rule on whether they had to do so. The decision left open the possibility that the court might approve districts that were balanced by voting eligible population. The same arguments would presumably apply to apportionment (how many districts each state gets). So this might change in the future.