Background In resource-limited settings where HIV-1 is endemic, there is a need for simple, inexpensive but effective rapid methods for detecting recent infections and estimating incidence for the purposes of surveillance and management. We sort to determine possible reasons for reported misclassifications of recent HIV-1 seroconversion as determined with the S/LS assay in sub-Saharan Africa. Findings We used the modified Determine HIV-1/2 sensitive/less sensitive method for determining recent HIV-1 seroconversion to determine recent infections among ELISA repeat HIV-1 positive samples from blood donors. Furthermore, HIV-1 seropositivity was confirmed using a line immunoassay and the results used to validate the performance of the modified Determine HIV-1/2 S/LS assay. The results confirmed reported misclassifications of recent HIV-1 seroconversion in sub-Saharan Africa. It was noted that, lack of confirmation of HIV-1 seropositivity in suspected cases of HIV-1 contributed to misclassifications. Conclusions It was concluded that, with confirmation of HIV-1 seropositivity, the modified Determine HIV-1/2 S/LS assay will be a rapid and cost effective method for determining HIV-1 recent infections and estimating incidence in resource-limited settings. The need for detailed studies to validate simple methods for determining recent HIV-1 infections is emphasized.