My husband and I live in two different states. He lives and works in Kansas, my children and I live and work in Illinois. Can we file joint for federal and separate for state taxes?

Yes, no problem at all filing jointly.

Yes; in certain situations, it may benefit you to file MFSto completely separate the state taxes. This is not common, but can result in overall tax savings. If you and your spouse are filing a joint federal return but you work in or are residents of different states, you may need to file separate state returns.Sometimes this is required by state tax law; other times this is the only way you can prevent from taxing the nonresident spouse's income in the wrong state.You can use tax software to file separate state returns.

I have generally found that the states allow married couples who live in separate states to file jointly, but only be taxed on income earned within that state's borders, IF each spouses claims to be a resident of their respective states.

If both spouses claim residency to ONE state, then ALL income is taxes by THAT state, and you claim a tax credit for taxes paid to the non-resident state.

Either way, a competent tax professional can file the state returns correctly.