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I am considering using Joomla to help three non-profits get websites up.  As a professional developer I am concerned about whether a Joomla site will adhere to standards and will meet minimum accessibility guidelines. I have run validation checks on a lot of Joomla-built sites today and I'd say about 50% of them fail on an accessibiltiy check.  I do not know if this is a result of the template used, or changes that were made afterwards.
At this point I am also trying to decide whether to build the template from scratch, or use a template and modify it to fit their needs. 

Can any of you give me your opinions/experience with your template development and accessibility?

I wonder if I stand a better chance of it being accessible if I build the template from scratch?

In my opinion, the vast majority of accessibility problems are the result of adding poorly-coded 3rd party components, modules, etc.

While Joomla validates out of the box, it is not 100% accessible out of the box.  One of our regular contributors distributes "accessible Joomla" although I can't find the link.

Also there are contributions devoted to accessibility:http://extensions.joomla.org/index.php?option=com_mtree&task=listcats&cat_id=1754&Itemid=35

And finally, the template itself can impede accessibility.

A developer who has an accessible template, chooses extensions carefully or recodes them, and follows regular web standards can definitely have an accessible Joomla site.

I think this would be the link she was looking for.

http://forge.joomla.org/sf/projects/accessible_joomla