It might be advantageous from a tax standpoint to run a business through multiple entities. For example, a construction company might form a separate company to own and lease its trucks and equipment back to its related entities. Or a corporation might transfer appreciated property to an affiliated corporation in order to limit risk in case it is sued.
However, the IRS may look twice at an operation if it includes multiple business entities -- especially if recordkeeping and filing requirements aren't handled properly. One construction firm in Georgia discovered that lesson the hard way when it took deductions that actually belonged to one of its corporate affiliates.