The study was conducted to assess whether the introduction of an electronic patient records-based system affected hepatitis B vaccination completion rates and post-vaccination return rates, when compared to a paper-based system. Data were gathered for 3 groups of patients: those commencing vaccination (a) when paper records were in use (paper records group), (b) after electronic patient records were introduced (basic electronic patient records group) and (c) after electronic patient records were enhanced with recall (enhanced electronic patient records group). Compared to the paper records group, the third dose completion rates for patients managed using electronic patient records did not differ significantly: 74/119 (62.2%) paper vs. 58/98 (59.2%) basic electronic patient records, p = 0.652 and 89/130 (68.5%) enhanced electronic patient records, p = 0.298. On sub-group analysis, completion rates in patients of black ethnicity in the enhanced electronic patient records group were significantly higher than those in the paper records group: 16/19 (84.2%) paper vs. 11/23 (47.8%) enhanced electronic patient records, p = 0.014. Patients in the enhanced electronic patient records group were more likely than those in the paper records group to attend for anti-HBs levels: 61/130 (46.9%) vs. 39/119 (32.8%), p = 0.023.