Looking at the IRS guidelines for W2 forms and the HSA section, I found IRS documentation to support mhoran_psprep's answer.
- Employer's contribution should not appear in box 1, 3, nor 5 of the W2.
- Employee's contribution through a cafeteria plan that is believed to be excluded from income should not appear in box 1, 3, nor 5 of the W2.
- All employer contributions should be in box 12 of the W-2 with code "W".
- All employee contributions through a cafeteria plan should be in box 12 of the W-2 with code "W" also.
From: http://www.irs.gov/pub/irs-pdf/iw2w3.pdf
Health savings account (HSA). An employer's contribution (including
an employee's contributions through a cafeteria plan) to an
employee's HSA is not subject to federal income tax withholding or
social security, Medicare, or railroad retirement taxes (or FUTA
tax) if it is reasonable to believe at the time of the payment that
the contribution will be excludable from the employee's income.
However, if it is not reasonable to believe at the time of payment
that the contribution will be excludable from the employee's income,
employer contributions are subject to federal income tax
withholding, social security and Medicare taxes (or railroad
retirement taxes, if applicable), and FUTA tax and must be reported
in boxes 1, 3, and 5 (use box 14 if railroad retirement taxes apply),
and on Form 940, Employer's Annual Federal Unemployment (FUTA) Tax
Return.
You must report all employer contributions (including an
employee's contributions through a cafeteria plan) to an HSA in box
12 of Form W-2 with code W. Employer contributions to an HSA that are
not excludable from the income of the employee also must be reported
in boxes 1, 3, and 5. (Use box 14 if railroad retirement taxes
apply.)
An employee's contributions to an HSA (unless made through a
cafeteria plan) are includible in income as wages and are subject to
federal income tax withholding and social security and Medicare taxes
(or railroad retirement taxes, if applicable). Employee contributions
are deductible, within limits, on the employee's Form
1040. For more information about HSAs, see Notice 2004-2, Notice 2004-50, and Notice 2008-52. Notice 2004-2, 2004-2 I.R.B. 269, is
available at www.irs.gov/irb/ 2004-02_IRB/ar09.html. Notice 2004-50,
2004-33 I.R.B. 196, is available at www.irs.gov/irb/2004-33_IRB/
ar08.html. Notice 2008-52, 2008-25 I.R.B. 1166, is available at
www.irs.gov/irb/2008-25_IRB/ar10.html. Also see Form 8889, Health
Savings Accounts (HSAs), and Pub. 969.