Prevalence of HIV infection in the Philippines remains low. This may be partly due to reliance on passive reporting for surveillance. The algorithm for laboratory testing for HIV infection has become more stringent in the sense that the screening assays are repeated in the confirmatory centers, before Western Blot is performed. This has been due to the high rate of false positives before 2005. Nucleic Acid Amplification testing (NAAT) has been performed routinely for blood banking purposes in other countries. In a few pilot studies, it has proven useful in identifying those cases in the early stage of the infection, which are missed on testing by antibody-based assays. The assay may prove useful in knowing whether false negatives happen with the current testing algorithm in the Philippines. Coupled with the detuned assay, identification of new cases may be critical for prevention of transmission, surveillance of cases, and early medical management if needed.