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Background  The physical inactivity pandemic and related non-communicable diseases have made it imperative for medical doctors (MDs) to effectively provide lifestyle counseling as part of prevention and treatment plans for patients. A one-day certification workshop was designed to improve MDs PA prescription knowledge, as part of the Exercise is Medicine® (EIM®) global health initiative. The objective was to determine knowledge gain of MDs participating in a standardized, one-day PA prescription workshop performed throughout Latin America (LA).    Methods  A 20-question multiple-choice test on PA topics, based on international guidelines, was completed before and after the workshop. Pre and post-test analyses, without a control group, were performed on 1044 MDs after the 8-h workshop that was delivered 41 times across 12 LA countries, from January 2014 to January 2015. Knowledge improvement was determined using the class-average normalized gain and individual relative gain. T-tests with 95% confidence interval levels were conducted to analyze differences between MD specialties.    Results  Test scores improved on average from 67 to 82% after the workshop ( p  <0.001). The average total individual relative gain was 29% [CI: 26 to 32%]. Relative gain by country ranged from 9.3% [CI: 2 to 16%; Nicaragua] to 73% [CI: 47 to 98%; Dominican Republic]. The mean of the 41 workshops’ class-average normalized gain was 46% [CI: 42 to 51%]. The largest groups of participants were general practitioners (GPs) (33%;  n  = 348), internal medicine (19%;  n  = 194), and family medicine (9% n  = 92) specialists. Relative gain for GPs was not different than for all grouped primary care specialties (30% vs. 27%,  p  =0.48). The knowledge gain was higher for the workshop modules on screening/risk stratification and prescription (43% [CI: 39–48%] and 38% [CI: 34–42%], than for the module on PA benefits and risks (26% [CI: 23–28%]).    Conclusion  This one-day workshop had a positive impact on the knowledge gain of MD’s on the topic of PA prescription. Although all groups of specialties increased knowledge, GPs and family medicine MDs benefited the most. This short course is an effective continuing education strategy for teaching PA assessment, counseling and prescription to MDs in Latin America, a topic rarely included in the training of MD’s in the region and the world. Further follow-up is needed to ascertain impact on PA counseling practices.    Electronic supplementary material  The online version of this article (doi:10.1186/s12889-016-3883-2) contains supplementary material, which is available to authorized users.

One-day workshop-based training improves physical activity prescription knowledge in Latin American physicians: a pre-test post-test study