According to many Rishonim, a person who merely needs to urinate may do so while wearing tefillin if he is not in a beis hakiseh kavua. A minority view is stringent, and one should follow this opinion. If one does remove them, they may be held, as long as the above-mentioned concern of becoming unclean does not apply. If he will be leaving the tefillin on, he should be careful to unravel the straps of the shel yad around his hand before tending to his needs.
סעיף א-ג, ס"ק י-טו, וביה"ל ד"ה בית־הכסא קבוע
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