Itemizing deductions refers to personal deductions, such as medical expenses and charitable contributions, not business expenses. Your spouse will still be able to deduct business expenses from his 1099-MISC business income even if you file separate tax returns. Note that as far as personal deductions go, when using the Married Filing Separately status if your spouse files and itemizes deductions you must also itemize deductions. The Married Filing Separately status can also result in the loss of certain credits. See the FAQ below for more information.
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