Few studies have compared outcomes of right colectomy (RC) and left colectomy (LC) with respect to both benign and malignant disease. The objective of this study was to compare outcomes of RC versus LC for benign and malignant disease using a national administrative database of academic medical centers. Using International Classification of Diseases, 9th Revision diagnosis and procedure codes, data was obtained from the University HealthSystem Consortium Clinical Data Base for patients that underwent RC and LC for benign and malignant disease between 2002 and 2006. The main outcomes compared were demographics, length of hospital stay, observed to expected in-hospital mortality, complications, 30-day readmission, and mean cost. There were a total of 27,483 patients; 12,971 patients (47.2%) underwent RC. Compared with LC for benign disease, RC was associated with a shorter length of stay, lower overall complications, lower wound infections, lower 30-day readmissions, and lower cost. Compared with LC for malignant disease, RC was associated with lower overall complications, lower wound infections, and lower cost. In this analysis of academic centers, RC was associated with a lower length of stay, lower morbidity, and lower cost when compared with LC for benign and malignant disease.