Medical students face the threat of needle stick injury with the consequent risk of acquiring blood-borne infection by pathogens such as HIV, Hepatitis B and Hepatitis C while performing their clinical activities in the hospitals. A cross-sectional study was conducted among 417 final year medical students from Universiti Kebangsaan Malaysia (UKM), University Malaya (UM) and Universiti Putra Malaysia (UPM). The aims of the study were to determine the incidence of cases and episodes of needle stick injury among them in the past year. This study was also done to find out the factors that might be associated with the occurrence of this problem. The factors were sociodemographic factors, duration of exposure, level of knowledge of blood-borne diseases and Universal Precaution, perception of risk of blood-borne diseases and level of practice of Universal Precaution. The incidence of needle stick injury among medical students was 14.1% (59 cases). The total number of episodes of needle stick injury was 87 and the incidence of episodes among respondents was high i.e. 20.9%. The highest incidence of episodes of needle stick injury occurred in Obstetric & Gynaecology postings, followed by Medicine and Surgery. For clinical procedures, venepuncture had the highest incidence followed by setting up drips and giving parenteral injections. The results showed the students who had needle stick injury (cases) had lower scores in the practice of Universal Precautions than non-cases (p<0.05). There was a significant association between the level of practice of Universal Precautions and the number of episodes of needle stick injury, i.e. the higher the score for the practice of Universal Precautions, the lower the number of episodes (beta=-2.03 x 10(-2), p<0.05). This study showed that medical students are at risk of needle stick injury and blood-borne infections during their clinical activities while performing procedures on patients especially for those who were poor at practising Universal Precautions. Therefore some preventive measures should be taken by the management of the universities and medical students to avoid the occurrence of these problems.