Introduction: Karate and Jiu-Jitsu are martial arts sharing a common origin but showing distinct movement biomechanics. The main features of Shotokan Karate are the impact blows, whereas JiuJitsu utilizes projections, strangulations, torsions and immobilizations. These differences can provoke different sites of lesion. Objective: To verify the frequency of lesions in Karate and Jiu-Jitsu and confront their respective lesions between the two studied groups. Methods: Ninety-four athletes from three different competitive levels (international, national and state) were transversally evaluated through an open-closed-question questionnaire. Data regarding starting age and period of training were also assessed. The T-Student test and Chi-Square test were applied for the group comparison. Statistically significant differences were considered when p<0,05. Results: 148 lesions were reported from a sample of 53 karate players, and 160 lesions from 41 Jiu-Jitsu athletes. The most frequency site of lesion in karate was the hands and fingers (15.5%) and, in Jiu-Jitsu, the knees (16.3%). The places which presented significant differences between the two groups were: legs (p=0.042), mouth and teeth (p=0,028), neck (p=0,038), shoulder (p=0,000), elbow (p=0,001), and ear (p=0,000). Conclusion: Karate and Jiu-Jitsu show differences as regards frequency and incidence of lesion sites. These findings contribute to the elaboration of specific preventive and therapeutic measures for each sport.