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I want to run an expenses by category report.
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category?
If you mean by account, which is what intuit for some really strange reason re-named the accounts in the chart of accounts (one ONE page only) - run a P&L, customize it to only show expenses
in the chart of accounts you can run a report on each account separately if you want
If you mean category in the products & services list, you can not, they are place holders to organize the list
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