For 2010, Medicare's Physician Quality Reporting Initiative (PQRI) offers three options for reporting, although not all three options apply to all measures:

• Claims-based reporting. Most - but not all - measures are reportable via claims. Some are reportable only through a registry.
• Registry-based reporting. The Centers for Medicare & Medicaid Services (CMS) has designated some measures as reportable only via an approved registry (PDF), such as the TMA-endorsed DocSite. The CMS's measure specifications manual for claims and registry reporting (PDF /ZIP)  includes a chart of individual measures that indicates by "C" and "R" whether you can report the measure via claims and/or registry.
• Electronic health record (EHR)-based reporting. These 10 measures are available for EHR-based reporting: diabetes measures 1, 2 and 3; heart failure measure 5; coronary artery disease measure 7; preventive measures 110, 111, 112 and 113; and HIT measure 124. CMS' 2010 EHR Measure Specifications (PDF) gives details.