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I sent my application to a Professor for a PhD position. His secretary replied:

Dear Mr Singh,

Many thanks for your application.

We will be in contact with you in due course.

Yours sincerely,

XXX XXX

What reply should I give to the secretary?

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Don't send any reply. They told you they received your application and will contact you when they're ready. There's nothing for you to say, and any email you send with a non-message will just clutter their inbox and waste their time. Unless you have something of substance to say or a question you need answered, don't send them anything.

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Don't send anything. They have explicitly told you that they will contact you.

They are not expecting an acknowledgement. They do not need an acknowledgement. If you didn't get their email, they would expect you to follow up, so the assumption is you received it, until you prove otherwise with a follow up email.

Some may say that it's always a good idea to acknowledge communication. It's true where there may be concern from the sender that the message has not been received, or an acknowledgement has been asked for.

It is almost completely inconsequential if you didn't receive their email, but the consequences of them not receiving your email are far far greater. Which is why it was acknowledged by them.

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    I have read your answer. – Acccumulation Jul 14 at 21:11
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    @Accumulation Please note that I have seen your comment. – Gregory Currie Jul 15 at 1:30
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    I'm not sure if this is required (?), I would have thought it wasn't, but since y'all doin it now: I have read all comments above – Lamar Latrell Jul 15 at 8:20
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    @GregoryCurrie Just writing to confirm that I found your exchange amusing – Michael Jul 15 at 9:48
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    "Some may say that it's always a good idea to acknowledge communication" -- in protocol terms, you don't ACK an ACK. Unless for humorous effect. – Steve Jessop Jul 15 at 12:38
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File it away - either in your trash can or, if you are closely tracking the status of all your job applications, in a relevant folder.

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If the "thank you for your application" message was the first e-mail they sent you, it is worth replying to confirm round-trip communication. It can be a very simple quote of their message with "Thank you" added.

If you have already established that the secretary is sending to the right e-mail address do not clutter their mailbox with a message that adds nothing to their information.

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You are not mandated to send any response, however, a thank-you response does not harm. You can reply with something like

Dear XXX,

Thanks for the acknowledgement. I will wait to hear back from you. Meanwhile, if you need any further information, I'd be happy to provide the same.

Regards,

Rishab.

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    Personally, I find this overly chatty. If we tell you, we will contact you, we don't need a response from you. The secretary probably wrote this to a large number of applicants. If a significant fraction of these reply, this just clutters their inbox. I'd consider it more polite to not answer emails that clearly don't require an answer. – Roland Jul 14 at 7:30
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    Good communication includes the acknowledgement of the information received. In this case, the info is that XXX will contact OP at some time in the future. Although not required, it would not hurt either to sent a short answer. Mail can be de-cluttered by deleting the unnecessary comm. +1 – virolino Jul 14 at 8:59
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    @virolino The problem with acknowledgement is that when does it end? How do you know they've received your acknowledgement of their acknowledgement? In this instance they are almost certainly not expecting an acknowledgement from you, so next to no information is getting transferred. – Gregory Currie Jul 14 at 11:32
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    @virolino The secretary’s message is the acknowledgement. You say all communication needs acknowledgement, and that itself implies that an acknowledgement is not communcation! Otherwise you just described an infinite loop. Also, since “just hit delete” is a guaranteed cure-all for e-clutter, please, PM me your email address, so I can add you to “a few” email lists. It’s no bother for you, since you can just hit “delete”. – Harper - Reinstate Monica Jul 14 at 17:50
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    @virolino People who follow your advice get blocked as pests in functioning communities. Unless you have absolute evidence that the group you are dealing with expects pointless and time wasting replies of the kind you suggest then do not engage in this behavior. I will guarantee you that a lot of people you are replying to you hate that you do so and will be happy if you stop. – jwpfox Jul 14 at 19:37
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It is important to note that in most cases these days "thanks for your application" messages are automated emails generated by the company's online hiring portal. That email is just to confirm that the hiring portal worked as intended and that the company is now able to review your application when they get to it.

Not only do you not need to respond to it, but there is a good chance that if you do respond that your message will go to an unmonitored email address and never be read.

If you need to follow up with the employer, make sure not to rely on that email's reply address to establish a point of contact. Instead see the job listing itself for if it contains contact info.

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