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I requested a reference from a prof whom I used to know . He politely declined my request and responded this way:

Hmmm..it is tricky - since I have not taught you or worked with you - it would be very hard for me to say anything about your work in a fair and honest manner. I believe that you have done very good work - but you must understand that only someone who has worked with you or taught you can give a strong recommendation - one that will convince the reviewers.

If I give you a recommendation - it will have very little value since I would have only an indirect knowledge of your work and would not be able to write convincingly. I hope you can understand.

I hope you understand why I am reluctant to write a letter for you.

I wish you all the best.

I feel this is totally fair and what he said is right. I want to thank him for the long email he wrote to decline my request in a nice and kind manner. How should I go about it?

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    Maybe a simple "You make a good point, thanks!" – FrustratedWithFormsDesigner Mar 6 '14 at 4:45
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    I fail to see the issue in writing a thank you mail/letter. Could you elaborate on the problem you have with it? – CMW Mar 6 '14 at 7:33
  • If you were looking for a personal recommendation (as opposed to a professional one), then you can reply and explain that. Otherwise, I'm with @shaan. – Bobson Mar 6 '14 at 16:09
  • Say, "Thank you!" If you want to have more interaction with this person, then look for ways you can work with him or for him. Otherwise, express your gratitude & move on. – sea-rob Mar 6 '14 at 16:32
  • Also note that he tells you that you should ask a person who has taught you or worked with you for such a letter. Perhaps you should consider that, to get what you need? – Thorbjørn Ravn Andersen Mar 7 '14 at 14:59
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It's good see that you have taken your rejection in a positive way and you are not complaining about it.

You can respond to him if you wish as I mentioned below:

Thank you prof for your valuable reply. You are right in saying "NO" to my request for recommendation as I felt that I made a mistake in asking recommendation after reading your reply, where you are right that you may find it difficult in recommending me for a job without knowing about my work.

I hope that I did not made you uncomfortable by asking for your recommendation.

Once again, thank you for your honest reply prof.

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Since your prof has said more than once "I hope you understand" it would be nice if you provide that reassurance:

Thankyou, I do understand and I see your point (or agree with you)

The question remains why you asked for a reference from someone who doesn't know you well enough to write one. Were you just collecting dozens of references in case you need them? Or are you unable to think of who to ask? In that case, you might go on to say

I asked you because ...

and then ask

Can you suggest someone that would be a better choice?

(Don't take this opportunity to ask "can you change your mind?" - that would not be polite at all.)

You should both open your letter with thanks (Dear Professor X, thank you for your kind email and detailed explanation) and close it that way (thanks again for considering my request and explaining your reasoning, which I now understand). Notice the extra bonus statement of understanding - your prof really did mention this an extraordinary amount so be sure to say more than once that you do understand.

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If you are a friend or a colleague of this person, then a polite "Thank you for responding to my email" and nothing more might be the best course of action. If the professor is not someone with whom you are socially or emotionally close, then simply not responding might be the better course of action. Not every email or returned missive requires a response.

You may wish to reflect upon why you thought that this person would be willing to provide a recommendation for you and then to your surprise did not. Perhaps you should reevaluate your relationship (if any) with this person or reassess your strengths or weaknesses in your field of endeavor. Most people understand how difficult it can be to start off in the business world, so a rejection of a reference is almost always a sign that they don't have confidence in the rejectee's abilities or that the person asked for the reference isn't the supportive person who you considered them to be.

Either way, unless you feel strongly that there is a need to respond, not doing so may be the safest option for you.

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