As the year draws to a close, tax departments have more to worry about than just the fiscal cliff and potential tax hikes.

Companies are preparing to close the books on 2012, and this year a new set of companies will be swept into reporting uncertain tax positions. That means tax departments are busy shoring up uncertainties and planning how they will deal with varied unresolved tax issues.

The end of 2012 marks a reporting milestone for companies with assets of at least $50 million, which will be required for the first time to include with their corporate tax returns Schedule ...