Background <p>Removable appliances greatly affect oral hygiene and increase the amount of plaque retention. The aim of this prospective study was to evaluate the effects of anterior crossbite treatment with Z-spring appliance and clear aligners on periodontal health and salivary parameters.</p> Methods <p>Thirty children aged 7–12 years were divided into two equal groups for anterior crossbite treatment: Clear aligners (Aligner group) and Z-spring appliance (Z-spring group). Periodontal health was assessed using plaque index (PI), gingival index (GI), and bleeding on probing (BOP). Salivary flow rate, pH, and buffering capacity were also measured. Assessments were performed at baseline (T0) and post-treatment (T1).</p> Results <p>Aligner group exhibited significant increases in PI (<i>p</i> = 0.003) and GI (<i>p</i> = 0.002) scores, alongside a reduction in salivary buffering capacity (<i>p</i> = 0.039). Z-spring group demonstrated significant increases in unstimulated (<i>p</i> = 0.008) and stimulated salivary pH (<i>p</i> = 0.008). Intergroup comparisons revealed higher PI (<i>p</i> = 0.002) and GI (<i>p</i> = 0.003) scores in Aligner group, while Z-spring group showed increased stimulated salivary flow rate (<i>p</i> = 0.039).</p> Conclusions <p>Clear aligner treatment negatively affected oral hygiene in children within a short treatment period. This study is the first to compare Z-spring appliances and clear aligners for anterior crossbite correction, providing novel insights into their effects on oral health.</p> Trial registration <p>ClinicalTrials.gov NCT06858033. Retrospectively registered 20/01/2025.</p>