Background HIV-infected men have higher rates of delayed diagnosis, reduced antiretroviral treatment (ART) retention and mortality than women. We aimed to assess, by gender, the first two UNAIDS 90 targets in rural southern Mozambique. Methods This analysis was embedded in a larger prospective cohort enrolling individuals with new HIV diagnosis between May 2014-June 2015 from clinic and home-based testing (HBT). We assessed gender differences between steps of the HIV-cascade. Adjusted HIV-community prevalence was estimated using multiple imputation (MI). Results Among 11,773 adults randomized in HBT (7084 female and 4689 male), the response rate before HIV testing was 48.7% among eligible men and 62.0% among women (p Conclusion The contribution of missing HIV-serostatus data differentially impacted indicators of HIV prevalence and of achievement of UNAIDS targets by age and gender and men were missing long before the second 90. Increased efforts to characterize missing men and their needs will and their needs will allow us to urgently address the barriers to men accessing care and ensure men are not left behind in the UNAIDS 90-90-90 targets achievement.