Abstract Background Focal epithelial hyperplasia (FEH) is a rare oral HPV‐related disease, highly prevalent in certain ethnic communities. A previous study found 7.5% prevalence among school children from the Indian community Embera‐Chamí in Colombia. Objective To determine the prevalence and Human Papillomavirus (HPVs)‐type in children with FEH. Materials and methods One hundred and thirty‐eight students were screened. All FEH samples were HPV‐tested by two PCR‐based systems. Results We identified 18 FEH cases. β‐globin amplification was obtained in 15 cases and nine were HPV‐55‐positive by the HPV‐PCR‐hybridization method. Nine cases (50%) were HPV‐13‐positive by the GP5+/GP6+‐based method. Twelve cases (80%) were HPV‐positive by one or the other method. Forty‐four percent and 88% of interviewed parents reported family histories of FEH and toothbrush sharing, respectively. Conclusions Human Papillomavirus‐DNA was identified in the majority of FEH cases and HPV‐13 was the only genotype involved. Frequent familiar infection suggests interfamiliar transmission, genetic predisposition or infection susceptibility among family members.