Only 50% of New Yorkers aged 50 and over reported ever being screened for colorectal cancer by any modality according to a recent household survey. The objective of this investigation was to assess the impact of a hospital-based intervention aimed at eliminating health care system barriers to timely colorectal cancer screening at Lincoln Medical Center, a large, urban public hospital in one of the nation's poorest census tracts. We conducted a retrospective analysis of all colonoscopies performed over an 11-month period, during which a multi-pronged intervention to increase the number of screening colonoscopies took place. Two "patient navigators" were hired during the study period to provide continuity for colonoscopy patients. A Direct Endoscopic Referral System (DERS) was also implemented. Enhancements to the gastrointestinal (GI) suite were also made to improve operational efficiency. Immediately following the introduction of the patient navigators, there was a dramatic and sustained decline in the broken appointment rates for both screening and diagnostic colonoscopy (from 67% in May of 2003 to 5% in June of 2003). The likelihood of keeping the appointment for colonoscopy after the patient navigator intervention increased by nearly 3-fold (relative risk = 2.6, 95% CI 2.2-3.0). The rate of screening colonoscopies increased from 56.8 per month to 119 per month. The screening colonoscopy coverage provided by this facility among persons aged 50 and over in surrounding Zip codes increased from 5.2 to 15.6% (RR 3.0, 95% CI 1.9-4.7). Efforts to increase the number of screening colonoscopies were highly successful, due in large part to the influence of patient navigators, a streamlined referral system, and GI suite enhancements. These findings suggest that there are significant health-care system barriers to colonoscopy that, when addressed, could have a significant impact on screening colonoscopy rates in the general population.