Background Sometimes, it seems to be difficult to preserve the aberrant hepatic artery (HA) during pancreaticoduodenectomy (PD), with respect to en bloc lymph node dissection, especially in the case of aberrant right hepatic artery (RHA). Therefore, we evaluated the influence of incomplete en bloc lymph node (LN) dissection when aberrant RHA arises. Methods We reviewed 103 patients with mid-to-distal common bile duct (CBD) cancers who underwent PD by one surgeon at Asan Medical Center from December 1994 to November 2005 (73 men, 30 women; mean age, 61.1 ± 9.4 (range: 40-84) years). The mean follow-up period was 32.7 months. We compared the normal RHA group with the aberrant RHA group. Results Eighty-eight cases showed normal RHA anatomy, including nine cases (8.7%) of aberrant left hepatic artery (LHA) with normal RHA cases (normal HA group). RHA anomalies were observed in 15 cases (14.6%, aberrant HA group). In all cases, there was no direct invasion of cancer to aberrant HA. Among two groups, 43 cases (41.7%) showed recurrence and there was no significant difference in recurrence between two groups (p = 0.202). Three-year and 5-year overall survivals were 33.3% and 28.5% in the normal HA group, whereas 47.1% and 28.3% in the aberrant RHA group, respectively. There also was no statistically significant difference in survival (p = 0.763). Conclusions When performing PD for CBD cancer, aberrant RHA should be preserved if there was no cancerous invasion and it does not seem to affect the recurrence of disease and overall survival of patients.