BACKGROUND: Large-scale randomized clinical trials are needed to assess the role of Roux-en-Y gastric bypass (RYGB) in treating patients with type 2 diabetes mellitus (T2DM). Recruitment challenges must be understood. METHODS: One hundred twenty participants were needed for a prospective randomized controlled trial investigating treatments for hyperglycemia and cardiovascular disease risk factors in patients with T2DM. The trial had two arms-intensive medical management plus a rigorous lifestyle intervention (LS/IMM) versus LS/IMM with RYGB. Medical inclusion criteria included glycosylated hemoglobin (HbA1c) >/=8.0 % while under the care of a physician and body mass index (BMI) 30.0-39.9 kg/m(2). Another inclusion criterion was expressed willingness to accept randomization and participate fully. Varied recruitment strategies were employed at four academic hospitals in the USA and Taiwan, including referrals, mass media, direct mail to patients drawn from a practice-based database, and direct mail to commercial mailing lists. RESULTS: Between February 2008 and December 2011, 2,648 candidates were phone-screened and 240 were screened on site; 120 participants were eventually randomized. Impediments included stringent medical inclusion criteria and a lack of equipoise (i.e., strong beliefs or preferences) among patients and their personal community-based physicians. To meet timeline requirements, the upper limit for BMI was increased from 34.9 to 39.9 kg/m(2) and an additional site was added. CONCLUSIONS: We successfully recruited 120 participants with poorly controlled T2DM and mild to moderate obesity. Participants had to be willing to accept randomization to either surgical or nonsurgical treatments. Recruitment took 4 years.