What are long-term side effects of taking accutane?

Relatively safe/few. The following study documented that the long term effects of Accutane were relatively minor and safe. These were related to skin and mucous membranes ~5% and include xeroderma (dry skin), dry eyes, arthralgias (joint aches) and aggravation of eczema. For further details see: http://www.Ncbi.Nlm.Nih.Gov/pubmed/7918010.
Rare. Long term side effects are rare but occasionally people may have trouble tolerating contact lenses or it may aggravate inflammatory bowel problems. It does not affect your child bearing potential.