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But what about Medicare tax? As an independent contractor will he be required to pay that, too?

Yes. The self-employment tax is a combination of social security and medicare. The rate is 15.3% of his net income from self-employment. If he gets over the maximum wages for social security (about $85-90k) the self-employment tax also drops to just the Medicare rate, which is 2.9%.

Is it reasonable to run his hourly rate and hours through www.paycheckcity.com and save the amount they show for taxes (with the Social Security amount doubled)?

I suppose that would be a rather inexact way of doing it. Just make sure to double the medicare tax as well.

And all these taxes are only on his net business income, right? (He's going to be fronting travel expenses, then getting reimbursed -- I'd hate to think he has to pay Social Security and Medicare on the expense reimbursements!)

Right. He can deduct any other expenses he incurs as well - perhaps some auto, telephone, office supplies, etc.

--Peter
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