Background: In a faculty that searches to qualify the formation it gives, it is of relevance to analyze the multi-causal factors, inside as much as outside of the university, that affect the motivation and academic permanency. Materials and methods: a cross-sectional study was made with a population of 559 students from first to tenth semester registered in the Faculty of Medicine of the University of Manizales (Manizales, Colombia) in the year 2010. The representative sample was of 210 students. An anonymous survey was applied to identify some of the personal and social factors that could be demotivating or even generate academic desertion. Results: It was found that only 52.7% of the students feel some kind of institutional support, 75.2% refer to some kind of abuse and 52.4% said to have felt some kind of sexual harassment. 79.5% suffer from stress and most of them a moderate form and 17.4% say to have used psychoactive substances such as amphetamines. Conclusions: It is concluded that no institutional support, sexual harassment and stress are found between the factors that affect academic motivation and are of incidence in the high quantity (almost 50%) of students have contemplated the possibility of abandoning their studies. Almost halve of the populations does not perceives institutional support, three quarters say to feel some kind of abuse and nearly halve have felt being victims of harassment, mostly verbal and indirect; a high number feel subjected to moderate stress levels.