Head lice infestations are common amongst school children in many countries. In Israel, over the last two decades, control strategies have focused on the use of pyrethroids. Control failure was reported in several areas of the country two years after introduction of permethrin to the market. In the present study lice were collected from children from nine primary schools in six neighborhoods in Jerusalem. The overall prevalence of head lice infestation was 11%, while 93% of the examined lice were found to be resistant to permethrin. The 3 earlier described point mutations involved in a knockdown resistance, i.e., M815I, T929I and I932F were used to detect resistance. Lice with 3 mutated sites were the most dominant haplotype detected (60%), while lice with 2 mutated sites (T929I and I932F) accounted for 31% of those sequenced. All point mutations existed on both alleles of the voltage gated sodium channel α-subunit locus.