I filled taxes self employed but didn't pay quarterly taxes will they reject my return

[ChristinaS]

No, returns aren't rejected based on something that you didn't do. If you didn't make quarterly payments, and should have, then your return will show that you owe money. Returns aren't rejected because you owe money. Returns are rejected due to mistakes, like wrong birth dates or children that were claimed on other tax returns.

If you don't pay in enough taxes without making estimated payments, then you need to do something about that going forward. You can't make estimated payments for 2016 now. But you can prevent a problem in 2017.