Stealth is correct, of course. If you are a contractor and receiving a 1099, you are not an employee. Whether you are correctly classified is a moot point for the purpose of this question, however, since it is possible for a contractor to be paid by direct deposit. It is not, however, required, and it is absolutely legal for employees to be paid by direct deposit and not contractors. It is also legal for different classes of employee to be paid differently; if the employer wanted to pay the home office by direct deposit and not the branch offices, or to pay managers and above by direct deposit and not anyone below manager, or to pay the Accounting department by direct deposit and pay Research and Development by paper check, all of those divisions would be legal because no law says it cannot be done that way.