We do confirmations in conjunction with our external auditor. Many times we actually confirm more than they ask for.
Without pulling out the workpapers, I would guess that we confirm the following:
1-2% of the number of deposit accounts; positive on large accounts and public funds, negative on the rest. We will probably confirm a much deeper penetration of dormant accounts in the future, on a positive basis.
25-30% of the dollar amount of loans. Large loans over a certain threshold are positively confirmed and returned directly to the external auditor. Smaller loans are sampled and negatively confirmed. We stratify everything below the large loan threshold into different ranges and take different samples in each (i.e. 10% of the dollar volume for loans between $500M and $750M, 5% of loans between $100M and $500M, etc.). All participations purchased and sold are confirmed.
While all of confirmations provide some benefit / assurance, I believe, from a risk and materiality standpoint, the large loan and deposit accounts, public accounts, participations and dormant accounts are the most important. On your samples, be sure and use statistically valid sampling techniques so you can extrapolate your findings to the entire portfolio.
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My opinions are just that...my opinions.