Background: The actual burden of dental caries prevalence varies with the caries assessment tool used. Therefore, the present study evaluated the caries diagnostic potentials of Decayed, Missing and Filled Teeth (DMFT); International Caries Detection and Assessment System (ICDAS) II and Caries Assessment Spectrum and Treatment (CAST) indices in estimating the caries prevalence rate of first permanent molar (FPM) in Saudi male children aged 7–9 years. Methods: This descriptive, cross-sectional study included 390 children by multistage stratified cluster sampling method in Al-Jouf Province, Saudi Arabia. The prevalence rates of FPM caries were determined by DMFT, ICDAS II and CAST indices at various diagnostic cut-off points. Intra- and inter-examiner reliability was determined. Results: The prevalence rates of FPM caries determined by DMFT (decayed), ICDAS II (codes 1–6) and CAST (codes 3–7) were 64.4% (61.6–67.2), 71.5% (69.2–73.2) and 71.0% (68.7–73.3), respectively. The prevalence rates of FPM caries determined by ICDAS II at various diagnostic cut-offs were as follows: ‘sound’ (code ‘0’), 28.5% (26.3–30.8); ‘enamel caries’ (codes 1–3), 57.2% (54.7–59.7) and ‘dentinal caries’ (codes 4–6), 14.3% (12.6–16.1). Similarly, the prevalence rates estimated by CAST at different diagnostic cut-off points were: ‘healthy’ (scores 0–2), 28.1% (25.9–30.4); ‘premorbid’ (score 3, enamel carious), 56.5% (54.0–59.0); ‘morbid’ (scores 4–5, cavitated carious dentin), 7.9% (6.6–9.3); ‘severe morbidity’ (scores 6–7, pulp exposure/fistula/abscess), 6.6% (5.4–8.1) and ‘mortality’ (score 8, lost), 0.8% (0.4–1.4). Conclusion: Enamel caries lesions were found in more than half of the FPMs investigated in the current study. CAST index is preferable because it detects the complete spectrum of caries. ICDAS II at codes 1–6 and CAST at codes 3–7 projected similar caries prevalence rates in FPMs.