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Dental materials with antibacterial properties can prevent the harmful effects caused by oral cariogenic bacteria. This double-blind controlled clinical trial evaluated the performance of a glass ionomer cement (GIC) added with antibiotics for sealing infected dentin in atraumatic restorations of primary molars. The study enrolled 45 children (45 teeth) between 5 and 8 years of age, of both genders, divided into two groups: GC (n=22), where cavities were lined with a conventional GIC (Vidrion F) and GA (n=23), with cavities lined with Vidrion F added with 1% each of metronidazole, ciprofloxacin and cefaclor antibiotic. Both groups were restored with Ketac Molar Easymix. Molars with carious lesions on the inner half of dentin without clinical or radiographic pulp damage were selected. Patients were evaluated clinically (pain, fistulas or mobility) and radiographically (area of caries, periapical region and furcation) after 1, 3, 6 and 12 months. For statistical analysis, chi-squared or Fisher's exact tests were used with a 5% significance level. GA (82.6-95.7%) had better results than GC (12.5-36.4%) in all evaluations (p<0.05) and the difference in the success rate was 46.2-72.5% higher for GA. The use of the antibiotic-containing GIC liner on infected dentin proved satisfactory when applied in deciduous teeth.