The purpose of this study was to compare the clinical performance of a resin-reinforced self-cured glass ionomer cement to a standard composite resin in a split mouth design, by using both systems for direct bonding of orthodontic stainless steel brackets in every patient. Forty eight patients (34 females and 14 males, of which 29 were adults > 18 years of age) with fixed appliances were followed for a mean period of 10 months (range 4-16 months). The performance of 864 stainless steel brackets was evaluated: 404 brackets were bonded with GC Fuji Ortho glass ionomer cement (GC Industrial, Tokyo, Japan) onto teeth soaked with water, and 460 were bonded with System 1+ composite resin (Ormco, Glendora, CA). System 1+ recorded an overall failure rate (18.2%) significantly higher (p < 0.05) than GC Fuji Ortho (7.9%). There were no statistically significant differences (p > 0.05) between the failure rates in the upper and lower arches with either material. Both in the upper and lower arches, System 1+ exhibited a failure rate significantly higher (p < 0.05) than GC Fuji Ortho. When the bonding performance of the six anterior teeth was compared with first and second premolars, no statistically significant differences were found (p > 0.05) between bonding agents in either arch. System 1+ exhibited a failure rate significantly higher (p < 0.05) than GC Fuji Ortho, both in the anterior and posterior segments. Both bonding agents failed mainly at the enamel-adhesive interface, without causing any damage to the enamel.