BackgroundMany medical research projects encounter difficulties. The objective of this study was to assess the self-reported frequency of difficulties encountered by medical researchers while conducting research and to identify factors associated with their occurrence.MethodsThe authors conducted a cross-sectional survey in 2010 among principal investigators of 996 study protocols approved by the Research Ethics Committee in Geneva, Switzerland, between 2001 and 2005. The authors asked principal investigators to rate the level of difficulty (1: none, to 5: very great) encountered across the research process.Results588 questionnaires were sent back (participation rate 59.0 %). 391 (66.5 %) studies were completed at the time of the survey. Investigators reported that the most frequent difficulties were related to patient enrollment (44.3 %), data collection (26.7 %), data analysis and interpretation (21.5 %), collaboration with caregivers (21.0 %), study design (20.4 %), publication in peer-reviewed journal (20.2 %), hiring of competent study personnel (20.2 %), and getting funding (19.2 %). On average, investigators reported 2.8 difficulties per project (SD 2.8, range 0 to 12). In multivariable analysis, the number of difficulties was higher for studies initiated by public sponsors (vs. private), single center studies (vs. multicenter), and studies about treatment, diagnosis or prognosis (i.e., clinical vs. other studies).ConclusionsMedical researchers reported substantial logistical difficulties in conducting clinical research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12874-016-0151-1) contains supplementary material, which is available to authorized users.