One of the girls died in September when she was taken off life support.
The parents tried to stop the move, but the courts sided with doctors who said it was best to let the brain-dead child die.
Charges against the couple include aggravated assault, criminal negligence causing bodily harm and failing to provide the necessities of life.
They were arrested after paramedics called to their home in May found the two-year-old twins suffering from injuries and severe malnourishment.
A bail decision is expected within three weeks.
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