Seeking Refuge with Allah from Shaitaan
["a uthu billahi minash Shaitaanir Rajeem" ]
From Tafseer lecture notes given at Omm Al Qura University, Makkah 1993
Acknowledgement: Omm Rafiq
Allah, t'ala has instructed us to seek refuge in Him (isti atha ) in the beginning of each reading of Quran by saying: 
"When you read the Qur'ân, seek refuge in Allah from the rejected Shaitan".
That is, if you want to read Qur‘ân, seek refuge in Allah beforehand.
The word a uthu means to take refuge and seek protection in something or someone. It is a common expression to say "I took refuge in this person" or I sought his protection." Allah, ta'ala said in the words of the Prophet Musa-peace be upon him:
"For me, I have sought safety and well-being with my Lord and Your Lord, against your injuring (stoning) me."
In other words -- I have taken shelter in and sought refuge in Allah against any injury or vilification of his enemy.
Shaitaan (Satan) in Arabic is a derivative of the word sha -ta-na which means "distanced". The devil is called this because of his distance from the truth and his rejection of it. It is a common misconception to think that the Shaitan and his followers (Shaiyateen) are Jinn only. They can be humans as proven by the words of Allah [Surat Al An'Am, Aya 112]
"Likewise did We make for every Messenger an enemy, -- Satans among men and Jinns"
It is reported that Omar, may Allah be pleased with him, rode a donkey and was deceived by it. It said, "Get down off of me. Verily you have ridden on Shaitan."
Ar-Rajeem- one who is rejected. The root is the word ra-ja-ma, which means the throwing of stones. Here this meaning of stoning refers to being killed, being cursed and expelled and insulted (shamed). This is the meaning we find in Surat Ash-Shu'araa, Aya 116 where it is said of Prophet Nuh (upon him be peace)
"They said: 'If thou desist not, O Noah, thou shalt be stoned (to death)"
Shaitan is rejected because he is cursed and expelled from the mercy of Allah.
According to the majority of the Islamic Scholars saying the isti'aatha is highly recommended before all reading of the Qur'ân with the exception of Salaat. However they do differ in opinion about its recitation at the beginning of Salaat.
Some feel that the isti'atha is mandatory and should be said in each rakat and others feel that to say it in the first rakat only is sufficient, considering the entire Salaat as 1 reading of Qur'ân. All of these scholars agree that the "isti'aatha", seeking refuge in Allah, is neither a part nor an ayat of the Qur'ân. The Prophet (peace be unto him) most frequently repeated the isti'aatha using the words:
"a uthu billahi minash Shaitaanir Rajeem"
however, it is reported that when the Prophet - peace be upon him - got up at night he began his Salaat with Takbir (Allahu Akbar) and then he said another version of the isti aatha which is: "I seek refuge in Allah, the All Hearing, All Knowing from the rejected and cursed Shaitan, from his prodding and his haughtiness and his invectives.
"A uthu billahi as-Sami'ul Aleem minal khuthi wal khbaaith war rujiz As Shaitaanir Rajeem"
Reference: Sunans of Abi Dawood and Ibn Maja and others
When the believer says this it means that he is seeking refuge in and the safeguard of Allah from Shaitan, the rejected being, so as not to harm him in his religion or in his life, or not to cause him to fail in an act that Allah has ordered him to do. As a result when you read the Qur'ân you come under the shield of Allah's protection and care and Shaitan turns away, flees and becomes busy with his plans.
By this saying, the isti'aatha, the Muslim is also asking the Creator, the All-Hearing, All-Knowing for protection against the winking (gesturing / posturing) and prodding and whispering of the devil, as verily Shaitan will only be prevented from hindering people with the help of the Lord of the Worlds.
1) This refers to one uninterrupted sitting. If, for example, you read Qur'ân and then stop to answer the telephone, when you resume your reading you should begin with the isti'aatha once again.
Allahumma, I seek refuge in You from knowledge that does not benefit, from a heart that is not subdued, from a supplication that is not answered, and from a soul that is not satisfied.