The recent reports by Institute of Medicine, `To Err is Human' and `Crossing Quality Chasm', revealed a large prevalence of medical errors and substandard care in US hospitals. Since then there has been a substantial increase in the efforts to measure and improve quality of care. The objective of this study was to compare the quality of care across hospitals using available performance indicators and examine the association between organizational factors and hospital performance. The main focus of this study was on important structural attributes of hospitals, namely - teaching status, location and market competition. The Nationwide Inpatient Sample for years 2003 and 2005, and the State Inpatient Database for years 2004 to 2006 were used for analyses. Two types of hospital performance indicators were examined to compare quality of care - Patient safety indicators developed by Agency for Healthcare Research and Quality, and process of care indicators developed by Centers for Medicare and Medicaid services. Multivariable regression analyses were performed using generalized estimating equations and random effects regression models. Several organizational factors as well as patient characteristics were included in the multivariable models as control variables. Overall, the results from this study showed an inconsistent relationship between teaching status, location of hospitals or market competition and quality of care in hospitals. In addition, the results demonstrated that isolating potential effects of hospital structure on outcomes requires controlling for the variation in patient characteristics, such as age and comorbidities, which increase patients' risk for incurring patient safety events. The findings from this study provide useful insight into the areas where the patient safety and quality initiatives should be focused. Moreover, the results identified the organizational factors that are relevant to certain types of hospitals and which should be considered before evaluating quality of care and enacting any policies about publicly reporting of performance or payment initiatives that are relevant to these hospitals.