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I had serious health problems during my BSc studies and got a very poor GPA of 2.88 to be exact. After that, (I think) I performed much better in MSc, got a 3.75 GPA, and published two peer-review journal articles.

Now, I am looking for Ph.D. positions and worried about my low BSc GPA. In fact, I applied for two positions and got rejected straightaway. I assume that it is because of my low BSc GPA. Should I explain the reason for my low GPA? If yes, should I write it in my SOP, cover letter, personal statement, or in any other separate document?

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    Apply to many more than two places! At least ten, possibly fifteen. – astronat May 1 at 12:48
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You need a sentence or less to get this idea across. "While illness affected my undergraduate performance, I overcame the issues as my MS performance demonstrates."

There are a lot of places for such a sentence depending on the application materials requested. Even the SOP might "host" it, provided that you make the SOP more about the future and your goals than about the past. But the personal statement, if required, is probably better. But a separate document might be rejected.

If you are required to provide letters of recommendation, make sure that the writers emphasize your current skills and ability to succeed. They don't need to mention the problems, but their impact should lead to the assumption that poor performance is not expected in future.

But having been rejected twice means little in the abstract. Perhaps they are just the wrong places for you. A broad approach (several institutions with varied reputations) is a better way to assure success than any narrowly focused program.

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