Objective To assess the prevalence of physical and sexual violence motivated by perception of sexual orientation and gender identity in sexual and gender minorities. Methods We searched nine databases without language restrictions for peer-reviewed and grey literature published from 2000 to April 2016. We included studies with more than 50 participants that measured the prevalence of physical and sexual violence perceived as being motivated by sexual orientation and gender identity or gender expression. We excluded intimate partner violence and self-harm. Due to heterogeneity and the absence of confidence intervals in most studies, we made no meta-analysis. Findings We included 76 articles from 50 countries. These covered 74 studies conducted between 1995 and 2014, including a total of 202 607 sexual and gender minority participants. The quality of data was relatively poor due to a lack of standardized measures and sometimes small and non-randomized samples. In studies where all sexual and gender minorities were analysed as one population, the prevalence of physical and sexual violence ranged from 6% (in a study including 240 people) to 25% (49/196 people) and 5.6% (28/504) to 11.4% (55/484), respectively. For transgender people the prevalence ranged from 11.8% (of a subsample of 34 people) to 68.2% (75/110) and 7.0% (in a study including 255 people) to 49.1% (54/110). Conclusion More data are needed on the prevalence, risk factors and consequences of physical and sexual violence motivated by sexual orientation and gender identity in different geographical and cultural settings. National violence prevention policies and interventions should include sexual and gender minorities.