The clinical and public health implication of HIV Western blot (WB) indeterminate results is yet to be appraised in sub-Saharan Africa, including Nigeria. Using HIV Tri Line Test enzyme-linked immunosorbent assay (ELISA), 1286 patients (600 males and 686 females; age range, 5-60 years) with symptoms suggestive of HIV infection were screened. A total of 1020 (79.3%, 95% confidence interval [CI] 76.8-81.5) of the patients comprising of 514 (85.7%) males and 506 (73.8%) females were HIV seropositive and the difference was statistical significantly (χ2 = 5.72, df = 1, p = 0.05). Western blot analysis of sera from the 1020 HIV-seropositve individuals using the BIO-RAD NEW LAV-BLOT I specifying World Health Organization (WHO) interpretive criteria, confirmed the HIV serostatus of 815 (79.9%, 95% CI, 77.4-82.4) of them with 205 (20.1%, 95% CI, 17.6-22.6) individuals having indeterminate results consisting of either; 1 env ± gag ± pol, gag + pol, gag only or pol only. Of these, 102 (19.8%) were males and 103 (20.4%) were females. Patients aged 11-20 years old recorded the highest percentage of indeterminate results (31.7%, 95% CI, 20.2-43.2) while those aged 21-30 years recorded the least (14.2%, 95% CI, 10.6-17.8) and the difference was statistically significant (χ2 = 15.73, df = 5, p = 0.05). Result confirmed the limitation of Western blot assays in HIV confirmatory serodiagnosis. After obtaining HIV indeterminate Western blot result, clinicians should consider the total profile for the patient, reassess risk factors for HIV infection, perform a HIV retesting at 3-month intervals for 6 months or use an alternate HIV antibody confirmatory assay and running antibody tests for other human retroviruses.