Abstract Background There is an increasingly growing trend towards integrating scientific research training into undergraduate medical education. Communication, research and organisational/learning skills are core competences acquired by scientific research activity. The aim of this study was to assess the perceived performance of a core of transversal skills, related with scientific research, by Portuguese medical students. Methods A cross-sectional study was conducted in 611 Portuguese students attending the first, fourth and sixth years of the medical course, during the same academic year. A validated questionnaire was applied for this purpose. Results Medical students felt confident regarding the majority of the analyzed transversal skills, particularly regarding team work capacity (72.7 % perceived their own capacity as good). On the other hand, the perceived ability to manage information technology, time and to search literature was classified only as sufficient by many of them. The progression over the medical course and participation in research activities were associated with an increasing odds of a good perceived performance of skills such as writing skills (research activity: OR = 2.00; 95 % CI: 1.34–2.97) and English proficiency (research activity: OR = 1.59; 95 % CI: 1.06–2.38/final year medical students: OR = 3.63; 95 % CI: 2.42–5.45). Conclusions In this line, the early exposure to research activities along undergraduate medical education is an added value for students and the implementation of an integrated research program on medical curriculum should be considered.