BackgroundGaps between evidence-based research and clinical-public health practice have been evident for decades. One of the aims of medical student research is to close this gap. Accordingly, evaluating individual and environmental factors that influence participation of medical students in research are needed to understand and identify potential targets for action. This study aims to identify characteristics of medical student researchers in Colombia and the associated factors with scientific publications.MethodsA cross-sectional study of Colombian medical students involved in research using a validated, self-administered, online survey. The survey was distributed through the Colombian Association of Medical Students’ Associations (ASCEMCOL). Data sets were analyzed using descriptive and summary statistics. Bivariate analysis and a multiple logistic regression model were conducted to identify predictors of scientific publications.ResultsA total of 133 responses were analyzed from students at 12 Colombian cities and 20 higher-education institutions. Although 94% of responders had at least one research proposal, only 57% had completed a project, and 17% had published their findings. Barriers for undertaking research included time restrictions and a lack of mentorship. Motivational factors included opportunity to publish findings and good mentorship. Students planning to do a specialization (OR = 3.25; 95% Confidence interval [CI] = 1.27–8.30), innovators (OR = 3.52; 95%CI = 1.30–9.52) and committed (OR = 3.39; 95%CI = 1.02–11.29), those who had previously published their findings (OR 9.13 IC95% 2.57–32.48), and were further in their medical education (OR 2.26 IC95% 1.01–5.07), were more likely to publish scientific papers.ConclusionsOur findings describe medical students understanding of the process of conducting research in Colombia. Although there appears to be motivation to participate in research, very few students achieve publication. Barriers such as time constraints and mentorship seem to play a critical role. This highlights opportunities where barriers to research can be overcome in medical school and other levels.Electronic supplementary materialThe online version of this article (10.1186/s12909-017-1087-9) contains supplementary material, which is available to authorized users.