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I have the option to choose either of those protocols to connect to my university WLAN. Which should I use? Does it matter? What are the drawbacks of each choice?

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I would use TTLS unless I had a reason not to. It's tried technology and supported across more platforms.

Here is a good (if somewhat long) overview over at O'Reilly. Be sure to read the comments to the article for more opinions.

A Technical Comparison of TTLS and PEAP

Here is a quote from the conclusion

Though there is not a large technical difference between the TTLS and PEAP protocols, TTLS has a number of slight advantages. In addition to a slight degree of flexibility at the protocol level, products are available now and support a much wider variety of client operating systems.

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