Objective The metrics used to assess quality of care and pay for performance in rheumatology are increasingly important. The Centers for Medicare and Medicaid Services established the Physician Quality Reporting System (PQRS) to allow physicians to report performance measures for many conditions, including osteoporosis and rheumatoid arthritis (RA). We described the frequency and nature of physician-reported reasons why recommended care for individual osteoporosis and RA patients was not provided. Methods Using national data on Medicare fee-for-service beneficiaries (2007-2009), we identified health care providers reporting on quality of care for any of 3 osteoporosis or 3 RA measures. PQRS reason codes allowed physicians to submit explanations why recommended care was not given. Results In 2009, 1,775 physicians reported on ≥1 osteoporosis PQRS measure and 630 physicians reported on ≥1 RA measure. For the older women whose physician reported on lifetime dual x-ray absorptiometry screening at least once since the age of 60 years via PQRS, 76% received such screening. Among the patients with physician-diagnosed osteoporosis reported via PQRS, 82% received prescription osteoporosis medication in the preceding year. For RA medication use reported via PQRS, 89% of patients received a disease-modifying antirheumatic drug or a biologic agent. For the remaining 11-24% of osteoporosis and RA patients, physicians reported medical, patient, system, or other reasons why care was considered but not provided. Conclusion A substantial fraction of Medicare enrollees who did not receive recommended osteoporosis or RA care had physician-documented reasons for why care was not provided. For Medicare and other health plans that implement penalties for apparent nonperformance or delivery of suboptimal care, it will be important to allow physicians to provide reasons that care was considered medically inappropriate, refused, or otherwise not feasible. © 2013 by the American College of Rheumatology.