The possible formation of brown recurrent common duct stones (RCS) as a long-term side effect of sphincterotomy (SPHT) has been evaluated in 63 patients with stone formation after cholecystectomy, 253 who underwent SPHT or choledocholithotomy, 131 with postoperative monitoring of bile bacteriologic characteristics through the T tube, and 20 with stone and bile analysis at both operations. In addition, findings are also reported in 145 patients who underwent surgical SPHT and radiologic review of up to 28 years after surgery, five who underwent ampullectomy, and 55 who underwent endoscopic SPHT. The RCS were usually brown (72.5% of cases), and were always associated with bile infection caused by Escherichia coli. Sixty-two percent of brown RCS were found after SPHT. Eleven percent of patients who underwent surgical SPHT, 9% who underwent endoscopic SPHT, and 66.6% who underwent ampullectomies had brown RCS. Sphincterotomy determined a fivefold greater incidence of postoperative bactibilia, and a seven-fold greater incidence of brown RCS, than did choledocholithotomy. It is suggested that: (1) since brown RCS are secondary to bile contamination from the duodenum, SPHT (and subsequent stricture), facilitating both bile contamination and bacterial overgrowth, could be considered a basic factor in the formation of these stones; and (2) since true RCS are mostly of the brown subtype, SPHT could prevent the occurrence of retained stones by flushing the stones that were missed during the first operation, but undoubtedly increases the total incidence of RCS.