In Vietnam, there have been reported to be highly incident cancer of nasopharynx. Epstein-Barr virus (EBV) have been considered to be mainly associated with nasopharyngeal carcinoma (NPC), in which EBV-encoded latent protein 1, 2 (LMP-1, LMP2) were found to be important factor target to NPC development. Thus, it is important to explore whether a non-invasive method could be applicable to screen and early diagnosis of NPC. In current study, NP (nasopharyngeal) and non-NP brushing samples were collected consecutively from participants when they underwent NP biopsy at Cho Ray Hospital, HCMC, Vietnam. PCR assay were used to detection of LMP-1, LMP-2 and T-test statistical analysis were used to analyze its diagnosis value. NP-brushing samples from NPC patients showed frequency of 45.00% and 60.00% for LMP-1 and LMP-2, respectively. Conversely, none of any cases of non-NP brushing samples were found to be positive to target both/individual genes. Virtually, in combination of both two genes, the frequency was increased to 66.67% as well as the PI value (PI ≥ 0.5). The p value < 0.05 (LMP-1: p = 0.037; LMP-2: p = 0.008; both: p = 0.004) was observed, that indicated the correlation of between the presence both LMP-1, LMP-2 and NPC. The specific value was 100.00% for each/both candidate genes. Moreover, a high odd ratio (OR) and relative risk (RR) were also calculated of each/both candidate genes. In the case of LMP-1, OR, RR were 25.6087 (95%CI = 01.3479 -486.545, p = 0.0309), 14.4762 (95%CI = 0.9085 -230.672, p = 0.00585), respectively; in the case of LMP-2, the OR, RR were 45.5882 (95%CI = 2.391 -869.201, p = 0.0111), 19.0476.11 (95%CI = 1.2166 -298.2256, p = 0.0358), respectively; both candidate genes, the OR and RR were 58.8000 (95%CI = 2.9081 -1070.6992, p = 0.0076), 26.5714 (95%CI = 1.3193 -320.7527, p = 0.0309), respectively. Due to those results, the detection of both LMP-1 and LMP-2 in NP brushing samples could be an effective supplement for NPC early diagnosis that being non-invasive and rapid, demonstrated great potential for screening the high-risk of NPC in Vietnamese population.