Objective <p>Endotoxin is a component of the outer membrane of gram-negative bacteria; it adheres to orthodontic brackets and contributes to inflammation of adjacent gingival tissues. This study investigated the effects of chlorhexidine (CHX) and appliance material on plaque control, gingivitis, and subgingival endotoxin activity during the initial phase of orthodontic treatment. Materials and Methods: Sixty-eight participants aged 12–18 years (50% females) were recruited and randomized into groups based on appliance material (metal vs. nonmetal) and CHX use. The plaque and gingival indices, plaque pH, and subgingival endotoxin activity were assessed before appliance placement (T0) and two months after the commencement of orthodontic treatment (T1).</p> Results <p>There were no significant differences in the changes in endotoxin activity, periodontal status, and plaque pH (ΔT1-T0) between the metal and nonmetal groups regardless of CHX usage. Gingivitis decreased in the nonmetal appliance group with standard oral hygiene (<i>p</i> = 0.033). Endotoxin activity at T1 was correlated with the extent of gingivitis (<i>r</i> = 0.459; <i>p</i> &lt; 0.001) and plaque accumulation (<i>r</i> = 0.264; <i>p</i> = 0.035). Multiple regression analysis revealed that after controlling for the effects of sex, appliance material, and CHX, the predictors of gingivitis after 2 months of orthodontic treatment were increased endotoxin activity (<i>p</i> = 0.004), increased plaque index (<i>p</i> = 0.005), and older age (<i>p</i> = 0.043).</p> Conclusion <p>The early impacts of metal and nonmetal orthodontic appliances on gingival inflammation and plaque accumulation are similar, with changes in the extent of gingivitis linked to endotoxin levels rather than appliance type or CHX use.</p> Clinical relevance <p>Gingivitis during orthodontic treatment is mostly related to efficient plaque control and not to appliance material.</p>