Clostridium perfringens infection causes subclinical and clinical necrotic enteritis in poultry flocks, and it is estimated to result in US$2 billion of losses worldwide every year. The aims of this study were to determine the incidence, toxin types, and antimicrobial resistance levels to C. perfringens isolated from premarket, 5-wk-old, clinically healthy broiler chickens in Taiwan, and to examine the relationships between intestinal lesions and the numbers of C. perfringens in intestinal contents. In total, 435 samples of chicken ileum contents were collected from 98 broiler farms during June 2012 to February 2013. The C. perfringens isolation rate was 9.9% (43/435). The positive rate of tested farms was 29.6% (29/98). All the isolates were C. perfringens type A, only possessing the cpa gene encoding for toxin α. No netB gene encoding NetB toxin associated with necrotic enteritis, and no cpe gene encoding for the C. perfringens enterotoxin causing human intestinal disorder were detected. A quantitative PCR analysis revealed that the mean C. perfringens number in the intestinal contents was 3.9 × 10⁶ colony-forming units (CFU)/g, ranging from 6.85 × 10² to 1.61 × 10⁷ CFU/g. The gross and histopathologic lesions revealed a positive correlation (p < 0.05) between lesion score and C. perfringens number in the ilea of C. perfringens–positive chickens. Antimicrobial susceptibility tests of all C. perfringens isolates indicated that the minimum inhibitory concentration inhibiting 50% of isolates (MIC₅₀) for amoxicillin, bacitracin, chlortetracycline, enrofloxacin, erythromycin, florfenicol, and lincomycin was ≤0.125, 0.5, 128, 0.25, ≥256, 2, and ≥256 μg/ml, respectively. Most of the C. perfringens isolates were susceptible to amoxicillin, bacitracin, and enrofloxacin but resistant to chlortetracycline, erythromycin, and lincomycin. Interestingly, C. perfringens isolated from chickens with severe lesions had higher MIC₅₀ for erythromycin and lincomycin than those isolates from chickens with mild lesions. Conclusively, reductions in both the incidence of C. perfringens infection on farms and the concentrations of C. perfringens in intestines to improve broiler health are still needed in Taiwan.