Successful execution of clinical and research studies of viral diseases caused by high-consequence pathogens requires careful consideration. Even with meticulous planning, significant challenges may arise and impact study timelines, data generation, and outcomes; also, austere environments can compound issues. In this chapter, we provide an overview of components of laboratory operations for vaccine studies of high-consequence pathogens in resource-limited settings, using real-world examples and lessons learned during Ebola virus-targeted vaccine trials in Western and Central Africa. We include common and less-recognized challenges encountered in laboratory operations during these studies. We describe challenges along five main axes: (1) infrastructure; (2) assays (including development and/or execution for study endpoints, exploratory research, and inclusion/exclusion criteria); (3) material and supply logistics; (4) biosafety and biosecurity (including specimen accountability); and (5) cultural aspects. Although laboratory-specific challenges may vary according to pathogen, study design, location, and environment, lessons learned in these studies have broad applicability to optimize planning and execution of laboratory-supported clinical trials of medical countermeasures in resource-limited settings.