Objectives To study the incidence of peri-implantitis over 13 years between two types of dental implants. Materials and methods Peri-implantitis incidence was defined as bone loss ≥ 1.0 mm after 1 year, and with BOP or suppuration. Results Nineteen subjects with TioBlast AstraTech™ (AT) and 22 subjects with machine-etched Brånemark Nobel Biocare® (NB) implants were studied. The incidences of peri-implantitis between years 1 and 7 and between years 7 and 13 were 26.2% and 7.1% for AT implants, and 30.4% and 11.5% for NB implants (NS). A history of periodontitis was a risk for future incidence of peri-implantitis (Likelihood ratio: 4.1, 95% CI: 2.0, 8.4, p < 0.001). Subjects with a history of systemic disease had a higher incidence of peri-implantitis (p < 0.05). Conclusions No difference in the incidence of peri-implantitis over a period of 13 years as an effect implant surface and design was found. Bone loss during the first 7 years after implant installation was greater than thereafter. Microbiological information at year 7 did not predict incidence of peri-implantitis at year 13. Subjects with a previous history of periodontitis and with systemic disease were at higher risk for future incidence of peri-implantitis.