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Can the Standard Deduction still apply to a Traditional IRA early withdrawal?
IRA distributions are reported on line 15b on the standard form 1040.  That is in the same Income section as most of your other income (including that 1099 income and W2 income, etc.).  Its income is included in the Line 22 "Total Income", from which the Personal Exemption (calculated on 6d, subtracted from the total in line 42) and the Standard Deduction (line 40 - also Itemized Deduction total would be here) are later reduced to arrive at Line 43, "Taxable Income". As such, yes, he might owe only the 10% penalty (which is reported on line 59, and you do not reduce this by the deductions, as you surmised).