.ח In Case of Emergency

רבי אבהו נפיק בין גברא לגברא

Although the גמרא seems to state quite casually that רבי אבהו would leave between עליות, it seems quite clear from the later פוסקים that this is only for a צורך גדול and should still be avoided if possible. The ערוך השלחן  או"ח קמ"ו:א goes so far as to suggest that קריאת התורה is at least at the same level of being in the middle of שמונה עשרה and thus, even if one has to go to the bathroom, he should wait it out to the best of his ability.