Abstract Introduction Different limb lengths are used in Roux-en-Y gastric bypass (RYGB) surgery, as there is no consensus which limb length strategy has the best outcomes. The biliopancreatic limb (BPL) is thought to play an important role in achieving weight loss and associated comorbidity resolution. The objective of this study was to assess the impact of a longer BPL on weight loss and comorbidity improvement at 5 years after primary RYGB. Methods All patients aged ≥ 18 years undergoing primary RYGB between 2014–2017 with registered follow-up 5 years after surgery were included. Long BPL was defined as BPL ≥ 100 cm and short BPL as BPL < 100 cm. The primary outcome was achieving at least 25% total weight loss (TWL) at 5 years. Secondary outcomes included absolute %TWL and improvement of comorbidities. A propensity score matched logistic and linear regression was used to estimate the difference in outcomes between patients with long and short BPL. Results At 5 years, long BPL had higher odds to achieve ≥ 25% TWL (odds ratio (OR) 1.19, 95% confidence interval (CI) 1.01 – 1.41) and was associated with 1.26% higher absolute TWL (β = 1.26, 95% CI 0.53 – 1.99). Furthermore, long BPL was more likely to result in improved diabetes mellitus (OR = 2.17, 95% CI 1.31 – 3.60) and hypertension (OR = 1.45, 95% CI 1.06 – 1.99). Conclusion Patients undergoing RYGB with longer BPL achieved higher weight loss and were more likely to achieve improvement of comorbidities at 5 years. Graphical Abstract