<p>Could someone tell me what the units the <code>SetTimeout(int)</code> method in the <code>ICriteria</code> interface uses?<br>
Is it milliseconds, seconds, minutes or other?</p>

I think it's seconds.  The NHibernate API closely mirrors Hibernate Core for Java, where the
Criteria.setTimeout(int)
method uses seconds as the units (see also
Statement.setQueryTimeout(int)
).
Also, after looking at some NHibernate source, it appears that it's using that value to set the timeout for the underlying ADO.NET query, which uses seconds.