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Recently, the use of skeletal anchors in conjunction with fixed functional appliances (FFAs) has been advocated to enhance skeletal changes and reduce proclination of the lower incisors.To compare the skeletal and dento-alveolar effects of the use of FFAs with and without skeletal anchorage (miniscrews or miniplates).Unrestricted electronic search of six databases and additional manual searches were performed up to July 2015.Randomized and prospective non-randomized controlled trials directly comparing the use of FFA with and without skeletal anchorage, and involving growing patients with Class II malocclusion.Skeletal and dento-alveolar outcomes data were extracted in pre-defined sheets to collect study characteristics by two authors independently. After evaluating risk of bias, the standardized mean differences (SMDs) and 95% confidence intervals (CIs) were calculated with random-effects models. Subgrouping was pre-planned on the basis of the skeletal anchorage type used. Additional subgroup analysis was performed on the basis of the type of FFA used and the study design.Seven studies were evaluated, and only five of which were included in the meta-analysis. The analysis included data from 157 Class II subjects (77 treated with FFA and skeletal anchorage, and 80 with FFA alone). Random-effects meta-analysis demonstrated no significant differences in the mandibular length and SNB angle changes [SMD = 1.98 (95% CI −0.11 to 4.07) and 1.20 (95% CI −0.37 to 2.77) respectively]. Significant differences were found between the inclination changes of lower and upper incisors [SMD = −1.43 (95% CI −2.59 to −0.27) and SMD = −1.04 (95% CI −1.57 to −0.51) respectively]. Subgroup differences were highly significant in most of the outcomes.The studies reviewed provide insufficient evidence to form a conclusion regarding the effects of the use of skeletal anchorage with FFA. The available weak evidence suggests that the use of skeletal anchorage with FFA has no superior skeletal effects but is able to reduce proclination of the lower incisors.