Capability gaps prioritization is an important task required in multiple research and acquisition programs in military and industrial settings. We used multi-criteria decision analysis to prioritize capability gaps for small arms identified in a small-arms-specific Department of Defense (DOD) Joint Capabilities Integration & Development System study as approved by the DOD Joint Service Small Arms Program in 2005. A criteria hierarchy was created for use in judging the importance of each gap, taking into account time frames, tasks, conditions, and standards established by military subject matter experts. Military respondents representing US Army, Marine, Navy, Air Force, Coast Guard and SOCOM then completed an online preference survey using pairwise comparisons of each criterion, and analytical hierarchy process was used to produce a gap prioritization for each respondent and service, as well as one overall ranking. The priority rankings have helped in informing program and funding allocation decisions. Copyright © 2010 John Wiley & Sons, Ltd.