Here is my itinerary, followed by my question:

X (a European city) --> New York, JFK
New York, JFK --> Y (a South American city)

Do I need to pass through the passport control at JFK if I purchase those two flights separately?

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    Unless X is Dublin or Shannon, which have preclearance, the answer is yes, you will have to clear immigration and customs. How you purchased the flights is irrelevant. – Nate Eldredge Jan 18 '18 at 4:25
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    @NateEldredge and you will have to clear U.S. passport control at some point even if you are departing from Dublin and Shannon (in that case, you would clear it at the respective preclearance facility). – ajd Jan 18 '18 at 5:52
  • @ajd correct; therefore, if X is Dublin or Shannon, the answer to the question is no, you will not "need to pass through the passport control at JFK." – phoog Jan 18 '18 at 7:30
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    @user5054 Yes, exactly. You'll pass through the same passport control and customs process as everyone else, picking up and dropping off any checked luggage, before going through security and proceeding to your gate for your next flight (changing terminals if necessary). – Zach Lipton Jan 18 '18 at 8:45
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    @ajd it may or may not be misleading, depending on the purpose in asking the question. – phoog Jan 18 '18 at 13:45

There are no transit areas in US airports. Pathways through US immigration are the same regardless of whether you are leaving the airport immediately afterwards, taking a domestic connection, or taking an international connection. Thus, you need to have appropriate documentation to enter the US for whatever is your intended purpose (in your case, transit).

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    Also to add, you may have a hard time getting a free connection if you miss your connecting flight by purchasing your tickets separately – BritishSam Jan 18 '18 at 14:54

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