You can, but the results will need to be collated manually and you would have to setup an assignment to allow your students to submit their answers.
If you are running a questionnaire within Moodle, it is best to use the feedback module (which will be part of Moodle 2.0 when it is released). You'll need to install this module (unless you are already using Moodle 2.0, which you shouldn't be!). Instructions on how to do this can be found here:
More information on the feedback module can be found in MoodleDocs:
Hope this helps,