The study examined the association between the levels of inflammatory cytokines in the peri-implant crevicular fluid (PICF) and the development of peri-implant diseases in 111 patients (157 implants), of whom 65.8% were men with a mean age of 60.6 ± 7.1 years. Three months after dental implant surgery, the mean levels of IL-1β, IL-6 and TNF-α in PICF were 20.8 (15.0–23.4), 3.7 (2.6–5.0) and 13.7 (11.8–16.0) pg/ml, respectively. After 12 months, the incidence of peri-implant mucositis was 14.4% (16/111 patients) and peri-implantitis 6.3% (7/111 patients). In univariate logistic regression analyses, IL-1β and IL-6 were associated with both peri-implant mucositis and peri-implantitis (all p < 0.05). In multivariate analyses, only IL-1β remained a significant predictor (both p < 0.05). For IL-1β > 25 pg/mL, ROC curve analysis yielded areas under the curve of 0.833 (p < 0.0001) for mucositis and 0.804 (p = 0.0094) for peri-implantitis. The early level of IL-1β in PICF can thus serve as a potential predictor of peri-implant diseases after 12 months.