Introduction: The national algorithm for the diagnosis of HIV infection in Togo leads sometimes to discordant or indeterminate results. The objective of this study was to explore the characteristics of discordant and indeterminate HIV serologies at the National Reference Center for HIV testing (CNR-VIH) in Togo. Material and methods: Through a cross-sectional study, we analyzed the cases of discordant and indeterminate serologies from 2016 to 2018 at the CNR-VIH. Three kind of tests were used. The first one is a screening test also called “test 1” is very sensitive while the confirmatory test also called “test 2” is very specific and used when the sample is reactive with test 1. The third test is an immunoblotting test which is used in case of discordance between test 1 and test 2 results. We used Vironostika HIV Uni-Form II Ag/Ab (BioMerieux, Geneva, Switzerland), Determine Alere HIV-1/2 Serum/Plasma (Chiba, Japan) and Murex HIV Ag/Ab (Dartford, UK) as test 1 while Tri-Dot HIV-I/II (J. Mitra & Pvt Ltd. New Delhi-110-India Co.) and Inno-Lia HIV-I/II Score (Fujirebio, Ghent, Belgium) were used respectively as test 2 and test 3. The test 3 allowed us to determine the antibodies involved in the occurrence of indeterminate serologies. A pool of indeterminate samples was tested for qualitative detection of HIV-1 RNA by RT-PCR using the NucliSENS EasyQ HIV-1 platform from BioMérieux. Results: A total of 555 discordant serologies corresponding to 4.3% of all serologies performed over the 3 years have been analyzed. The average age of the subjects tested was 36.9 ± 17.4 years and men were slightly more represented with a sex ratio of 1.03. Of the 555 samples, 81 (14.7%) were reactive with 53 (9.6%) cases of HIV-1 and 28 (5.1%) cases of HIV-2. Two hundred and thirty-one (41.6%) samples were negative while the remaining 243 (43.8%) were indeterminate. The frequencies of antibodies (Ab) against gp120, gp41, p24, p31, p17, gp105 and gp36 were respectively 10.3%, 46.3%, 15.5 %, 11.2%, 8.8%, 5.4% and 5.0%. Among the 257 cases for which gp41 Ab had been detected, 202 (78.6%) were cases of indeterminate serology with the only presence of gp41 Ab. Qualitative HIV-1 RNA testing on 71 (29.2%) indeterminate samples was negative. Conclusion: This study showed that discordant serologies are frequently found in our common practice in Togo. The use of immunoblotting tests has the advantage of making it possible to elucidate more than half of these discordant serologies. The contribution of molecular biology techniques is uncertain. The large majority of these indeterminate serologies are due to cross-reactions particularly with gp41. These indeterminate serologies require not only further studies for their understanding but also an update of HIV diagnosis algorithm in Togo.