Hospital Payment Improvement and Equity Act of 2006 - Directs the Secretary of Health and Human Services to establish a process under which a hospital may appeal its wage index classification under title XVIII (Medicare) of the Social Security Act and select another area within the state (or, at the Secretary's discretion, within a contiguous state) to which to be reclassified.
Prescribes special rules for: (1) a competitively disadvantaged hospital in a single-hospital Metropolitan Statistical Area (MSA) surrounded by rural counties; and (2) rehabilitation hospitals and rehabilitation units.