OBJECTIVE The purpose of this study is twofold: to assess the incidence and implications of complications unique to placing a freestanding polycarbonate peg in patients with hydroxyapatite implants and to compare the incidence of complications in these patients with the incidence in patients with non-pegged hydroxyapatite implants. METHODS This is a retrospective clinical case series of 103 patients who underwent hydroxyapatite implant insertion at our institution. The incidence of postoperative complications in patients who underwent freestanding polycarbonate pegging procedures (n = 21) and those who had not (n = 82) were compared. RESULTS One postoperative complication - infection - occurred in a significantly higher percentage of patients in the pegged group (42.9%, 9/21) compared with the non-pegged group (19.5%, 16/82), (p = 0.037). Fifteen of the 21 patients (71.4%) in the pegged group experienced complications unique to freestanding polycarbonate pegging. Overall, 95.2% (20/21) of patients in the pegged group experienced a complication compared with 58.5% (48/82) of patients in the non-pegged group, (p = 0.001). In addition, there was an average of 3.1 (66/21) complications per patient in the pegged group compared with an average of 1.9 (106/82) complications per patient in the non-pegged group (p = 0.010). CONCLUSIONS Patients who received a freestanding polycarbonate pegged implant had a high risk of experiencing complications unique to pegging, and therefore a significantly higher rate of complications overall when compared with patients whose implant was not pegged. In addition, patients who received a pegged implant had a higher incidence of infection. However, most patients retained their pegs despite complications.