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Background About 60% of new HIV infections occur in HIV sero-discordant couples as 30% of married HIV positives have negative spouse. Although HIV-discordant couples are at 10% annual risk of acquiring HIV infection and large number of new HIV infections occur in stable partnerships, most HIV prevention programs focus on reducing casual sexual partners, condom use, and increasing fidelity among married partners. The purpose is assessment of sero-discordance among couples and associated factors. Methods The study was facility based cross sectional survey of couples who tested for HIV in 2011 and lived together at least 1 year period. The sample size was 154 couples (308 individuals) and necessary ethical issues were considered. Results Among 152 couples (304 individuals) who received VCT, HIV sero-prevalence in this study was found to be 11(3.6%). The prevalence in females 8(5.3%) was higher than that in males 3(2.0%). Of all participants, 9(3.0%) were found to be sero-discordant, 2(0.7%) concordant positive and 293(96.4%) concordant negative. Of all couples 9(5.9%) were found to be sero-discordant, 2(1.3%) concordant positive and 141(92.8%) concordant negative. Of the 9 sero-discordant couples, the 7(4.6%) prevalence in females was higher than 2(1.3%) in males. And, among 9 discordant couples, 5 of them were premarital sex partner and the rest 4 were married couples. Premarital couples were significantly discordant than married couples, AOR = 1.68; 95%CI (1.36- 5.40). HIV discordance was also significantly associated with having number of two or more sexual partners than one sexual partner AOR = 4.06; 95%CI (2.41-10.13). Conclusion The study indicated high prevalence of HIV discordance and increased risk of vulnerability. Therefore, couples should be aware of their own and their partners’ sero-status before and after engagement. Again, the following risk reduction methods were recommended: education of discordant couples on 100% correct condom use, and if condom breaks, or if they forget to use, Post-Exposure Prophylaxis must be established; for those who are not volunteer to use condom and/or have a child, early initiation of ART to positive partner. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-893) contains supplementary material, which is available to authorized users.