In terms of all‐stage HCC diagnosis, the combination of AFP and EV‐MALAT1 showed the best AUC (0.911, 95% CI 0.864–0.958) in a model of HCC vs. nontumor, while the EV‐MALAT1 and EV‐SNHG1 combination showed the best AUC (0.887, 95% CI 0.828–0.945) in a model of HCC vs. CH/LC. This evidence concerns the gene AFP and laryngotracheoesophageal cleft.