Objective Condyloma acuminatum (CA) is a common, viral, sexually transmitted disease worldwide. Human papillomavirus (HPV) genotyping has important clinical implications for the treatment of CA. We developed a loop-mediated isothermal amplification (LAMP) method for the detection of HPV. Methods We collected 294 cervical scrape samples, including 30 HPV-6-positive, 30 HPV-11-positive, 22 HPV-16-positive, 20 HPV-42-positve, 30 HPV-43-positive, 20 HPV-44-positive and 142 HPV-negative samples. Tissues from 40 patients with a pathological diagnosis of CA were paraffin-embedded and analyzed by LAMP and Luminex. Hydroxynaphthol blue (HNB) and electrophoresis were used to detect the results of LAMP. Results LAMP and Luminex systems were compared in detecting six subtypes of HPV. LAMP reactions were specific for each subtype. The sensitivity of LAMP for HPV-6, as determined by the HNB indicator assay, was 1000 copies/tube. The kappa value between the two methods was 0.98 (HPV-6), 0.94 (HPV-11), 0.89 (HPV-43), 0.87 (HPV-42) 0.79 (HPV-16) and 0.68 (HPV-44). Among the 142 HPV-negative samples determined by the Luminex assay, HPV-6 was detected in eight and HPV-11 in one by LAMP. Among the 40 CA samples, the results of LAMP and Luminex were in agreement in 38 (95%). Conclusion The results of this study indicated that the LAMP assay with HNB is superior to the Luminex method in terms of sensitivity and specificity. The specificity of LAMP was 100% and the sensitivity of LAMP was 1000 copies/tube using HNB. LAMP is therefore a useful, quick and accurate method for the clinical diagnosis of HPV subtypes.