Allelic loss of chromosome 3p, including the 3p21.3 region, is found in 95–100% of primary nasopharyngeal carcinoma (NPC) biopsies, suggesting that this region should harbor some tumor suppressor genes (TSGs) closely related to NPC development. Several TSGs located at 3p21.3, such as RASSF1A, LTF and BLU, have been demonstrated to be involved in NPC development. LARS2 (leucyl-tRNA synthetase 2, mitochondrial) is another gene located in the chromosome 3 common eliminated region-1 (C3CER1) at 3p21.3. In this study, we focussed on the epigenetic and genetic alterations of LARS2 in NPC. The mRNA expression of LARS2 was detected in 36 NPC and 8 chronic nasopharyngitis (NP) tissues by semi-quantitative reverse transcription-polymerase chain reaction (RT–PCR) and real-time RT–PCR. Subsequently, the mutation, allelic loss, and methylation status of LARS2 were analysed by polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP), homozygous deletion (HD) analysis and methylation-specific polymerase chain reaction in primary NPC tissues. No expression or down-regulation of LARS2 was observed in 78% of primary NPC tissues. No mutations, assessed by PCR-SSCP and DNA sequencing, were found in the promoter region and exon 1 of LARS2 in NPC tissues, whereas HD was detected in 28% of NPC specimens at the LARS2 locus. In addition, hypermethylation of LARS2 was found in 64% of NPC samples but only in 12.5% of NP biopsies. Our data indicate that inactivation of LARS2 by both genetic and epigenetic mechanisms may be a common and important event in the carcinogenesis of NPC.