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Background: In many parts of the world, stark racial disparities in human immunodeficiency virus (HIV) prevalence, incidence, prevention, and care outcomes persist among gay, bisexual, and other men who have sex with men (MSM), with Black MSM significantly impacted in the United States (U.S.). Individual-level characteristics, including sexual behaviors and socioeconomic status, do not fully account for racial/ethnic disparities in HIV among MSM. We hypothesize that neighborhood contexts and network characteristics influence risk for HIV infection as well as HIV-related prevention and care behaviors. As such, the study design includes the use of real-time geospatial methods and in-depth assessments of multiple network typologies to investigate the impact of neighborhood and network-level factors on HIV prevention and treatment among Black MSM residing in longstanding priority HIV elimination areas in the U.S., namely Chicago, Illinois and in the Deep South (Jackson, Mississippi and New Orleans, Louisiana) ( n = 450, n = 50, and n = 100, respectively). We describe the design, sampling methods, data collection, data management methods, and preliminary findings of the ongoing 'Neighborhoods and Networks (N2) Cohort Study'. Methods/Design: N2 employs a prospective longitudinal design. The sample includes Black MSM participants in Chicago recruited via respondent-driven sampling and assessed every six months over two years of follow-up. Participants enrolled in Jackson and New Orleans are being recruited through existing health and community services and assessed every six months over one year of follow-up. Mobility within and between neighborhoods is being assessed using global positioning system (GPS) technology. Social and sexual networks among Black MSM are being studied through egocentric network inventories as well as newer methods of creating meso-level networks that involve social media (Facebook) and mobile phone contacts. Key HIV prevention outcomes such as pre-exposure prophylaxis (PrEP) care engagement, and HIV/STI (sexually transmitted infections) biomarkers will be examined at baseline and follow-up. Results: As of 31 December 2018, a total of 361 men were enrolled across all study sites: 259 in Chicago and 102 in the Deep South (75 in New Orleans and 27 in Jackson). At baseline, participants ranged in age from 17 to 65 years old (mean = 34.3, standard deviation = 5.1) with 123 men (34.1%) self-reported as HIV positive. While HIV treatment levels were similar between sites, men in the Deep South reported higher rates of adherence than men in Chicago (63.3% versus 49.4%, p = 0.03). Sexual risk profiles were mainly the same between men from different study sites, with 22.9% of men in Chicago and 28.9% in the Deep South reporting consistent condom use during vaginal and anal sex ( p = 0.26). Regarding their home neighborhoods, men in the Deep South were more likely than those in Chicago to characterize theirs as having a good reputation (43.1% versus 24.7%, p < 0.001) and as being safe (37.3% versus 21.2%, p = 0.002). Conclusions: The focus on Black MSM in the N2 Study will allow for a nuanced exploration of the attitudes, beliefs, behaviors, and practices of a diverse group of Black MSM. The study is also positioned to provide novel insight about neighborhood and network characteristics that influence HIV-related behaviors. A health equity framework ensures that Black MSM are not explicitly or implicitly deemed as deviant, disordered, or the non-reference group. Findings from N2 will provide guidance for the implementation of more impactful HIV prevention interventions that engage a diverse population of Black MSM as we work toward HIV elimination in the U.S.