Background Laparoscopic distal gastrectomy (LDG) is an established procedure for the treatment of early gastric cancer. Roux-en-Y (R-Y) or Billroth-I (B-I) reconstruction is generally performed after LDG in Japan. The aim of this retrospective cohort study was to compare the effectiveness of R-Y and B-I reconstructions and thereby determine which has better clinical outcomes. Methods We analyzed data from 172 patients with gastric cancer who underwent LDG. Reconstruction was done by R-Y in 83 patients and B-I in 89. All patients were followed up for 5 years. Evaluated variables included symptoms, nutritional status, endoscopic findings, gallstone formation, and later gastrointestinal complications. Results Scores for the amount of residue in the gastric stump, remnant gastritis, and bile reflux, calculated according to the ''residue, gastritis, bile'' scoring system, were significantly lower in the R-Y group (score 0 vs. 1 and more; p = 0.027, \0.001, and \0.001, respectively). The proportion of patients with reflux esophagitis was significantly lower in the R-Y group (p \ 0.001). Relative values (postoperative 5 years/preoperative) for body weight, serum albumin level, and total cholesterol level were similar in the two groups (p = 0.59, 0.56, and 0.34, respectively). Gallstone formation did not differ between the groups (p = 0.57). As for later complications, the incidence of gastrointestinal ulcer was 4.5 % in the B-I group, and that of ileus was 3.6 % in the R-Y group, but differences between the groups were not significant (p = 0.12, 0.11, respectively). Conclusions As compared with B-I, R-Y was associated with lower long-term incidences of both bile reflux into the gastric remnant and reflux esophagitis.