Two of the foremost issues in screening colonoscopy involve delivering quality and maximizing adenoma detection rates (ADR). Little is known about the impact of deep sedation on ADR. This study aims to compare the detection of advanced lesions during screening colonoscopy performed with moderate conscious sedation (MCS) versus deep sedation (DS). A retrospective cohort study was performed using the Clinical Outcomes Research Initiative database. Average risk screening colonoscopies performed January 2000 to December 2005 were examined for practice setting, patient demographics, and findings, including detection of a polyp >9 mm and suspected malignant lesions. A total of 104,868 colonoscopies were examined, 97% of which were performed with MCS. Univariate analysis demonstrated that more polyps of any size were detected with MCS (38 vs. 34%, p < 0.0001) and more advanced lesions were found with DS compared with MCS (7 vs. 6%, p = 0.01). When exclusively examining sites that performed DS > 10% for all procedures, a more significant increase in advanced lesion detection when using DS was observed (7.5 vs. 5.7%, p = 0.003). When adjusted for age, gender, race/ethnicity, site, prep quality, and ASA group, DS was 25% more likely to detect an advanced lesion. Our data suggest that use of DS may be associated with a higher rate of advanced lesion detection. However, this retrospective design has limitations that necessitate follow-up with prospective studies. These follow-up studies would be essential to support any change in the standard practices of sedation.