Abstract • Background: Late 2019, a new highly contagious corona-virus SARS-CoV-2 has emerged in Wuhan, China, causing within two month a pandemic with the highest disease burden in elderly and people with pre-existing medical conditions. The pandemic has highlighted that new and more flexible clinical trial approaches, such as trial platforms, are needed to assess the efficacy and safety of interventions in a timely manner. The two existing Swiss cohorts of immunocompromised patients (i.e. Swiss HIV Cohort Study (SHCS) and Swiss Transplant Cohort Study (STCS)) are an ideal foundation to set-up a trial platform in Switzerland leveraging routinely collected data. Within a newly founded trial platform we plan to assess the efficacy of the first two mRNA SARS-CoV-2 vaccines that reached market authorisation in Switzerland in the frame of a pilot randomised controlled trial (RCT) while at the same time assessing the functionality of the trial platform.• Methods: We will conduct a multicenter randomised controlled, open-label, 2-arm sub-study pilot trial of a platform trial nested into two Swiss cohorts. Patients included in the SHCS or the STCS will be eligible for randomization to either receiving the mRNA vaccine Comirnaty® (Pfizer / BioNTech) or the Covid-19 mRNA Vaccine Moderna®. The primary clinical outcome will be change in pan-lg antibody response (pan-Ig anti-S1-RBD; baseline vs. three months after first vaccination). The pilot study will also enable us to assess endpoints related to trial conduct feasibility (i.e. duration of RCT set-up; time of patient recruitment; patient consent rate; proportion of missing data). Assuming vaccine reactivity of 90% in both vaccine groups we power our trial, using a non-inferiority margin such that a 95% two-sided confidence interval excludes a difference in favour of the reference group of more than 10%. A sample size of 380 (190 in each treatment arm) is required for a statistical power of 90% and a type I error of 0.025. The study is funded by the Swiss National Science Foundation (National Research Program NRP 78, ‘Covid-19’). • Discussion: This study will provide crucial information about the efficacy and safety of the mRNA SARS-CoV-2 vaccines in HIV patients and organ transplant recipients. Furthermore, this project has the potential to pave the way for further platform trials in Switzerland.Trial registration: NCT04805125