OBJECTIVE There is evidence that patients experience more discomfort/pain after peri-implant probing than periodontal probing. However, there are several plausible factors to additionally influence this observation: e.g., implant type, age, smoking. Thus, this study was designed to compare discomfort/pain after periodontal and peri-implant probing in different implant types. METHODS Two dentists recruited and examined 80 patients, each of them exhibiting a dental implant with a contralateral natural tooth. Only two types of implants were included. Periodontal and peri-implant probing depths (PPD) and probing attachment level (PAL) were assessed. Whether implant or tooth were measured first was randomly assigned. Immediately after probing patients scored discomfort/pain using a visual analogue scale (VAS). RESULTS Eighty patients (median; lower/upper quartile: age 57; 47.5/65.5 years; 40 females, 11 smokers) were examined. With the exception of PPD and PAL at the deepest site as well as mean PPD (p < .05) clinical parameters (PAL, bleeding on probing, suppuration) were well balanced between implants and teeth. Peri-implant probing (VAS: 9.0; 5.0/17.0) caused significantly (p = .038) more discomfort/pain than periodontal probing (5.5; 2.0/13.5). This was confirmed by repeated measures analysis of variance adjusting for several factors (p = .011). CONCLUSIONS Peri-implant probing caused significantly more discomfort/pain than periodontal probing.