Both injectable silicone biomaterial (PTQ) and pyrolytic carbon-coated beads (Durasphere) have been shown to be effective in treating passive faecal incontinence due to internal sphincter dysfunction. This is a randomized study to evaluate their relative safety and efficacy. Forty patients (mean age 59.5 years vs 58.9 years) were randomized to have inter-sphincteric injection of PTQ or submucosal injection of Durasphere. Patients were assessed with anorectal physiology, endoanal ultrasound, a validated incontinence score and quality of life questionnaires. In the Durasphere group, complications included rectal pain (5%), erosion through rectal mucosa (10%), and type III hypersensitivity reaction (5%). No complications occurred in the PTQ group. Compared with PTQ, Durasphere group has a more rapid action, with improved continence at 2 weeks after injection. In both groups, faecal continence significantly improved 6 weeks after injection, and continued to improve significantly up to 6 months in both groups (P < 0.0001). At 6 weeks, 6 and 12 months after injection, significantly more PTQ patients achieved greater than 50% improvement in Wexner's continence score than Durasphere patients (respectively, P = 0.01; P < 0.0001; P = 0.001). There was a significant improvement in faecal incontinence quality of life scale and the 12-month physical health scale of Short Form-12 health survey in the PTQ group but not in the Durasphere group. In patients with internal sphincter dysfunction, injectable silicone biomaterial was safer and more effective than Durasphere.