A picture would help and also knowing what you feed the turtle and how its tank is set up. Diet, lighting and housing all play a part in how a young turtle's shell develops. If diet is lacking, lighting is poor and the housing is dry-the shell will be deformed. If the shell is deformed, internal organs may be affected as well.

I have a free online box turtle care book at www.boxturtlesite.info. Please check it out if you haven't already. It along with other care resources will help you fine tune your care to get the best results for your baby turtle.
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Tess Cook
www.boxturtlesite.info

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