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What is the biblical basis for the idea that it's okay to bring any doubts to God in prayer?

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Yes, this is acceptable. It is not only in prayers and not only in the Old Testament but in the New Testament too.

It is important to see that Jesus himself endorses a critical stance.

Thomas the Apostle speaks (John, 20, 25):

"I won't believe it unless I see the nail wounds in his hands, put my fingers into them, and place my hand into the wound in his side.

Jesus endorses this attitude and bothers to get back to Thomas to give him proof (John, 20, 27):

Then he said to Thomas, “Put your finger here, and look at my hands. Put your hand into the wound in my side. Don’t be faithless any longer. Believe!

And finally (John, 20, 29):

Then Jesus told him, “You believe because you have seen me.

So the Bible makes it very clear that Jesus wants us to not just be gullible but to demand proof. Neither of the Apostles was prepared to believe without a proof and Jesus respected that and had this very story been incorporated into the Bible for us.

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    In general I agree that Jesus satisfies our doubts, but your argument is somewhat un-creditable particularly in light of your incomplete quotation of John 20:29. The second half of the verse which you left out in your answer goes on "Blessed are those who have not seen and yet have believed." – Caleb Sep 4 '11 at 17:23
  • @Caleb: Thank you for your remark. You have to be very careful here: Jesus is saying this after he gave proof and he is saying this only unto him, i.e. Thomas, who believes already because he has the evidence right before his eyes; Jesus is not saying this unto us or to anybody else or in general!!! So this part is one of the clearest and most unambiguous parts in the Bible. Christians have to take Jesus' word literally here and not try to interpret it as it seems convenient. I even think it is one of the most pivotal parts of the Bible! – vonjd Sep 4 '11 at 21:29
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    If you are going to try to take Jesus at his word quoting a full sentence shouldn't hurt your focus. From your last comment I could quote "Jesus is not" and build a case that you don't believe Jesus exists, but it's hard for anybody to check if I rip out a half a statement like that. If what you are saying is legitimate, more context will not hurt your case. – Caleb Sep 4 '11 at 21:39
  • Caleb, this is true, sorry for not giving more context. I think that it doesn't matter what I think, but you must agree that it is kind of strange when even the Apostles, his long-standing followers and best friends, don't believe in Jesus being some kind of supernatural being, right? And Jesus bothers eagerly to show them all kind of proofs - why only to them and not to us? "Blessed are those who have not seen and yet have believed." - a very convenient position indeed, isn't it! I think this part of the Bible cries for us being skeptical and not gullible, would you not agree? – vonjd Sep 4 '11 at 21:46
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God's grace is such that you can just be honest. Consider Mark 9:24, one of my favourite NT verses:

'Immediately the boy’s father exclaimed, “I do believe; help me overcome my unbelief!”'

Doubt mixed with faith is natural. Jesus' response is not recorded – so apparently He was neither surprised nor condemning.

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Most of the Psalms are examples of this!

The Psalms express deep doubts about God – "where are you?", "Why are you letting your faithful people be oppressed?", "Why am I in such pain?", etc. You can find the full range of human emotion in the Psalms, expressed directly and honestly to God. If David can do it, we can do it.

  • "If David can do it, we can do it." Almost brings up an entire new question, if it weren't subjective! – DTest Sep 1 '11 at 18:43
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The very act of bringing a sincere doubt to God in prayer could be seen as an act of faith. Think of the opposite, having a doubt, and not bringing it the Lord in prayer because you "doubt" that he cares, "doubt" that he can hear you, or "doubt" him in General.

Do you see the element of faith overcoming when you bring your doubts to God in prayer?

The other Answers have some good scriptures. I especially like mark 9:24, posted by [Wikis]

'Immediately the boy’s father exclaimed, “I do believe; help me overcome my unbelief!”'

To finally answer your question

What is the biblical basis for the idea that it's okay to bring any doubts to God in prayer?

Here is some biblical basis, 1 Peter 5:7

7 casting all your care upon Him, for He cares for you.

I think doubts which are troubling you can certainly be considered "Cares". Peter admonishes us to give them to the Lord. How can we do this? Paul says in Philippians 4:6

6 Be anxious for nothing, but in everything by prayer and supplication, with thanksgiving, let your requests be made known to God;

Putting these all together, i think we begin to see a biblical basis for bringing our doubts to the Lord in faith.

--- Edit--- On a personal note, i would recommend taking your doubts right to the scripture, as well. you might be surprised how many of our "doubts" are dealt with directly in the Word, a great coupling with prayer. Talk to God (Prayer), and hear from God (reading the word)

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