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Rock Lee cannot use ninjutsu or genjutsu (for some reason), but he can use his chakra (as miroku2192 has pointed out). He can perform Tree Walking and Water Walking, and he does use chakra to reinforce his body (something every shinobi does in order to jump around, etc).
That being said, presumably he used speed to pass the Kawarimi and Bushin portion of the Genin Exam. And, I expect he used make-up for the Henge. Whatever the case, it is assumed that it was Gai's vouching for Lee which got him out of the Academy.
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