Rural Hospital Assistance Act of 2009

Rural Hospital Assistance Act of 2009 - Amends title XVIII (Medicare) of the Social Security Act with respect to the additional inpatient hospital service payment (payment adjustment) for low-volume hospitals (usually meaning a "subsection (d) hospital" located more than 25 road miles from another subsection (d) hospital and having less than 800 discharges during the fiscal year.)

(Generally, a subsection (d) hospital is an acute care hospital, particularly one that receives payments under Medicare's inpatient prospective payment system (IPPS) when providing covered inpatient services to eligible beneficiaries.)

Redefines low-volume hospital, for discharges occurring during FY2009 only, as a subsection (d) hospital located more than 15 (instead of 25) road miles from another subsection (d) hospital and having less than 1,500 (instead of 800) discharges of individuals entitled to, or enrolled for, Medicare part A (Hospital Insurance) benefits ("tweeners,'' or hospitals too large to be critical access hospitals, but too small to be financially viable under the Medicare hospital prospective payment system (PPS)).

Revises, for FY2010 only, the temporary applicable percentage in the formula for determining the payment adjustment for such hospitals.

Requires the use of the non-wage adjusted prospective payment rate (PPS) rate during FY2010 under the Medicare-dependent hospital (MDH) program.

Prescribes requirements for hospitals to qualify for a Medicare hospital exception to the prohibition on certain physician referrals to hospitals in which such physicians have an ownership or investment interest in the entity. (Eliminates the Medicare hospital exception for physician-owned hospitals, but provides a limited exception for existing facilities.)