To compare the clinical efficacies of subgingival glycine air polishing and ultrasonic scaling combined with 0.12% chlorhexidine rinsing on patients with early peri-implant diseases (peri-implant mucositis and early peri-implantitis). Twenty-two systemically healthy patients with totally 42 implants and early peri-implant diseases, were recruited in this study. The patients were randomly divided into the test group and the control group. Patients in the test group were treated with subgingival glycine air polishing and patients in the control group were treated with ultrasonic scalers combined with 0.12% chlorhexidine rinsing. Periodontal parameters such as probing depth, bleeding index, plaque index and clinical attachment loss, at baseline and 2 months after treatment, respectively, were collected and compared between the test and control groups. For the natural teeth, the parameters of probing depth, bleeding index, plaque index and attachment loss in the two groups were significantly improved after treatments (medians were 0.48 mm vs 0.22 mm, 1.00 vs-0.13, 0.38 vs 0.50, 0.48 mm vs 0.22 mm, respectively for test and control group). There was no statistical difference of median between the two groups after treatment except for that of the attachment loss (medians, 0.48 mm vs 0.22 mm, 0.034). For the implants, differences of parameters in the two groups at baseline were insignificant. After treatments, the probing depths significantly decreased by 0.67 mm and 0.33 mm in the test group and the control group, respectively. The inter-group differences, however, were insignificant. Significant difference of the bleeding index after treatment was found in the test group (0.019), but not in the control group. No adverse reactions were found on patients in the two groups after treatments. Efficacy of subgingival glycine air polishing and ultrasonic scaling combined with 0.12% chlorhexidine rinsing is competitive on patients with early peri-implant diseases. However, the former treatment may be more effective oncontrolling the early peri-implant inflammation.