I've had this problem. It's actually plantar fasciitis. It's an inflammation of the connective tissue in the bottom of your foot.
I found ice, stretching and taping by my podiatrist to be very helpful. Also buying good shoes that are feel good when you put them on and rotating my shoes every day or two.
Wikipedia has a good informative page about it.
It took about 6 months for mine to heal up completely. It's a long process! Hang in there.
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