BACKGROUND: An estimated one- to-two-thirds of new human immunodeficiency virus (HIV) infections among US men who have sex with men (MSM) occur within the context of primary partnerships. Despite this fact, there remains a lack of prevention interventions that focus on male sero-discordant dyads. Interventions that provide male couples with skills to manage HIV risk, and to support each other towards active engagement in HIV prevention and care, are urgently needed. OBJECTIVE: The objective of this paper is to describe the protocol for an innovative dyadic intervention (Stronger Together) that combines couples' HIV testing and dyadic adherence counseling to improve treatment adherence and engagement in care among HIV sero-discordant male couples in the United States. METHODS: The research activities involve a prospective randomized controlled trial (RCT) of approximately 165 venue- and clinic-recruited sero-discordant male couples (330 individuals: 165 HIV sero-negative and 165 HIV sero-positive). Couples randomized into the intervention arm receive couples' HIV counseling and testing plus dyadic adherence counseling, while those randomized to the control arm receive individual HIV counseling and testing. The study takes place in three cities: Atlanta, GA (study site Emory University); Boston, MA (study site The Fenway Institute); and Chicago, IL (study site Ann & Robert H. Lurie Children's Hospital of Chicago). Cohort recruitment began in 2015. Couples are followed prospectively for 24 months, with study assessments at baseline, 6, 12, 18, and 24 months. RESULTS: Stronger Together was launched in August 2014. To date, 160 couples (97% of the target enrollment) have been enrolled and randomized. The average retention rate across the three sites is 95%. Relationship dissolution has been relatively low, with only 13 couples breaking up during the RCT. Of the 13 couples who have broken up, 10 of the 13 HIV-positive partners have been retained in the cohort; none of these HIV-positive partners have enrolled new partners into the RCT. CONCLUSIONS: The intervention offers a unique opportunity for sero-discordant couples to support each other towards common HIV management goals by facilitating their development of tailored prevention plans via couples-based HIV testing and counseling, as well as problem-solving skills in Partner Strategies to Enhance Problem-solving Skills (STEPS). TRIAL REGISTRATION: ClinicalTrials.gov NCT01772992; https://clinicaltrials.gov/ct2/show/NCT01772992 (Archived by WebCite at http://www.webcitation.org/6szFBVk1R).