Background: New technologies have paved the way for newer fabrication techniques, such as rapid prototyping, which has gained popularity in the fabrication of several orthodontic appliances including retainers. Aim: To evaluate the stability, survival time and periodontal health associated with vacuum-formed retainers (VFRs), bonded retainers (BRs) and rapid prototype retainers (RPRs) over a period of 12 months in retention. Study design: Prospective clinical study. Methods: A total of 72 participants completing fixed orthodontic treatment were allocated to the following three groups by the investigators based upon their initial malocclusion, compliant and preferences: VFR; BR; and RPR. The primary outcome was Little’s Irregularity Index (LII). Other stability parameters, including arch length (AL), inter-canine width (ICW) and inter-molar width (IMW), were also assessed immediately after debonding (T0) and 12 months (T2) after debonding. In addition, survival time, and calculus index and gingival index (GI) were assessed. Results: LII showed a significant difference ( P = 0.00) between the groups and was increased in the VFR group (0.18 ± 0.22 mm) compared to the BR (0.03 ± 0.05 mm) and RPR (0.01 ± 0.03 mm) groups but was not clinically significant. The mean survival time of maxillary retainers was longest for the RPR group (220.63 days; 95% confidence interval [CI] = 194.1–247.16) but there was no significant difference between the three groups ( P = 0.43). The mean survival time of mandibular retainers was higher and the same for the VFR and RPR groups (240 days; 95% CI = 240–240) and there was no significant difference between the three groups ( P = 0.38). The calculus index score ( P = 0.00) was statistically significant between the groups, with an increased score for the BR group (0.33 ± 0.27) compared to the VFR (0.07 ± 0.16) and RPR (0.13 ± 0.22) groups. Similarly, the GI score ( P = 0.02) was statistically significant between the groups and was increased in the BR group (0.01 ± 0.19) compared to the VFR (−0.15 ± 0.18) and RPR (−0.06 ± 0.15) groups. The increase in calculus index and GI scores for the BR group were not clinically significant. Conclusion: There were no clinically significant differences between the three retainer groups in terms of stability, periodontal health and time to failure.