Programmatically render HTML in taxonomy term description
The taxonomy_term_data table, which is the entity table for taxonomy terms, has a format column which stores the name of a filter to apply to the description when rendered.

It's available as a property on the entity, so you can use:

taxonomy_term_save((object)array(
  'name' =&gt; $name,
  'description' =&gt; $t('&lt;h5&gt;My description.&lt;/h5&gt;&lt;p&gt;More info.&lt;/p&gt;'),
  'vid' =&gt; $vocab-&gt;vid,
  'format' =&gt; 'full_html',
));