Objective: Colony-stimulating factor (CSF)-1 and interleukin (IL)-34 are growth factors that regulate myeloid cell functions and support osteoclastogenesis. CSF-1 and IL-34 levels in peri-implant diseases are yet unknown. This study evaluated CSF-1, IL-34, and IL-1β levels in saliva and peri-implant crevicular fluid (PICF) from patients having mucositis or peri-implantitis, as well as their correlation to clinical parameters of disease. Material and methods: Forty-three patients were included (mean age 61.1 ± 8.4; 62.8% female), 20 having mucositis and 23 having peri-implantitis. Patients were clinically examined and unstimulated whole saliva and PICF were collected. Levels of CSF-1, IL-34, and IL-1β were determined by enzyme-linked immunosorbent assays. Results: CSF-1 levels were higher in PICF from peri-implantitis compared with mucositis patients (p = 0.028), whereas IL-34 levels showed no significant difference between the groups (p = 0.060). No significant difference was found in PICF IL-1β levels between the groups. Salivary levels of CSF-1 and IL-34 did not differ significantly between mucositis and peri-implantitis. No significant difference was observed in the salivary levels of IL-1β between groups (p = 0.061). CSF-1 and IL-1β correlated significantly in both saliva and PICF. CSF-1 levels in saliva correlated with its levels in PICF. PICF CSF-1 levels showed potential to discriminate between peri-implantitis and mucositis (AUC = 0.695, 95% CI 0.53–0.85; p = 0.029). Conclusion: Increased levels of CSF-1 in peri-implant crevicular fluid, but not in saliva, were found in peri-implantitis patients, which might aid to discriminate the early and late stages of peri-implant diseases.