Prayer starts and person needs to go to bathroom
Question

                If prayer starts (i.e. the iqama is called) and the person feels the call of 
nature, what should he do?
Praise be to Allah.He should go to the restroom and tend to the call of nature even 
  if this means he will miss the jama'at (congregational prayer). The 
  evidence: Abullah Bin Arqam said, "The Messenger of Allah  
  (peace be upon him) said: 'If one of you needed to go to the restroom and the 
  salaat starts, he should start with the restroom.' "1
From the book What Should You Do in 
  the Following Situations... ?
1 Abu Dawood 88 and Sahih 
  al-Jaami' 373.