BACKGROUND Amplification based HIV-1 viral load and genotypic resistance assays are expensive, technologically complex and may be difficult to implement in resource limited settings. Inexpensive, simpler assays are urgently needed. OBJECTIVE To determine the suitability of the ExaVir Load and ExaVir Drug assays for use in patient monitoring. METHODS Specimens from 108 adults were used to compare ExaVir Load HIV-1 RT to Amplicor HIV-1 Monitor HIV-1 RNA, and ExaVir Drug phenotype to HIV GenoSure genotype. RESULTS HIV-1 RT and HIV-1 RNA levels were comparable (Pearson correlation coefficient 0.83). Most (94%) had detectable results in both assays. The mean difference (HIV-1 RT minus HIV-1 RNA) was -0.21 log(10)cps/mLequiv. Relationship between HIV-1 RT and HIV-1 RNA was not affected by RT mutations, CD4 cell count, or efavirenz (EFV) or nevirapine (NVP) use. Phenotypes were generally consistent with genotype findings for EFV, but not for NVP. Most patients (93.9%) with phenotypic EFV resistance had at least one EFV mutation, while 78.0% of patients with phenotypic NVP resistance had at least one NVP mutation. Eleven of 49 samples tested for EFV susceptibility were found resistant (n=2) or with reduced susceptibility (n=9) despite the absence of genotypic resistance. Eleven of 45 samples tested for NVP susceptibility were found resistant (n=9) or with reduced susceptibility (n=2) with no evidence of genotypic mutations. CONCLUSIONS The ExaVir Load assay performed well and may be an alternative to amplification based techniques for HIV-1 RNA quantification. The ExaVir Drug assay for phenotypic resistance testing requires further evaluation, especially for NVP.