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Back Bay Station is technically closer, but South Station is on the Red Line subway (which MIT is also on). South Station is probably a better choice -- from Back Bay Station, you'd have to either switch subway lines or walk a bit to get to MIT.
Once you get to South Station, look for the Red Line inbound toward Alewife ($2). You'll take the train to Kendall/MIT Station, which is on the northeast edge of MIT's campus.
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