Background In 2012, the US Food and Drug Administration (FDA) required drug manufacturers to give advance notice of impending drug shortages. A survey of infectious diseases (ID) physicians was undertaken to determine the impact of this requirement and to follow-up on prior perceptions of ID physicians on shortages of antimicrobial agents. Methods We used a web-based survey of ID physician members of the Emerging Infections Network in 2016. Results Of the 701 of 1597 members (44%) who responded, 70% reported the need to modify their antimicrobial choice because of a shortage in the prior 2 years. A majority (73%) reported the shortages affected patient care or outcomes by the use of broader-spectrum (75%), more costly (58%), less effective second-line (45%), or more toxic agents (37%). The most commonly reported antimicrobials in short supply were piperacillin-tazobactam, ampicillin-sulbactam, meropenem, cefotaxime, and cefepime. Respondents learned of shortages from hospital notification, from a colleague, contact from pharmacy after ordering the agent in short supply, or FDA or other website. The antimicrobial stewardship programs (ASPs) of a majority (83%) of respondents’ institutions had developed approaches to deal with shortages. Although 71% indicated that communications were sufficient, most (87%) did not perceive any improvement in communications about shortages since the 2012 FDA requirement. Conclusions The persistence of antimicrobial agent shortages reported by ID physicians is disturbing as is the resulting need to use broader-spectrum or more toxic agents. The prominent role of ASPs in helping to deal with shortages, effective communication channels, and the lack of perceived improvement in FDA’s communication strategy merit further consideration.