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This question already has an answer here:

My problem is about missing the messages from the labeling. I have a organized labels in my Gmail account but some old messages have no label. I want to find and add them proper labels.

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marked as duplicate by ChrisF Feb 8 '13 at 22:41

This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question.

    
Closely related: webapps.stackexchange.com/questions/28081/… – Al E. Feb 8 '13 at 14:49

Assuming you want find messages that don't have any of the labels you've created, it's as simple as a search for:

has:nouserlabels

If you want to find all messages that don't have any label at all, not even the system labels, try searching for

has:nouserlabels -in:inbox -in:spam -in:trash

This last will give you any message that doesn't have any of your labels and is not in your inbox, spam folder, or deleted messages.

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