The goal of this study was to assess factors associated with hormonal emergency contraception (EC) awareness and acceptability among a sample of low-income Latino women receiving care in two university reproductive health clinics. A total of 297 Latino women, 18-43 years of age, completed a survey about EC awareness during a clinic visit, between January and May 2003. Those women with some degree of awareness (n = 73) also completed questions related to their acceptance of EC. Factors examined included language preference, demographic characteristics, pregnancy history, contraceptive use history and knowledge and concerns about EC usage. We found that only 41% of English-speaking and 17% of Spanish-speaking women had ever heard of EC [adjusted odds ratio (OR) = 2.9, confidence interval (CI): 1.3, 6.4]. Among those aware of EC, unwillingness to use this method was associated with low levels of knowledge about the EC mechanism of action, but not about the EC regimen (adjusted OR = 0.5; CI: 0.3, 0.9). Specific misconceptions underlying their objections included the belief that women are more likely to get pregnant in the beginning of their cycle compared to the middle (unadjusted OR = 6.3; CI: 1.8, 22.6), and a belief that EC prevents implantation rather than ovulation (unadjusted OR = 5.7; CI: 1.2, 28.1). The extent to which the women considered EC to be morally wrong depended on their misconceptions about the EC mechanism, not on their religious background. The link between expressed moral concerns and incorrect knowledge coupled with its lack of association to religiosity suggests that enhanced education can help to alleviate moral objections, thereby increasing potential usage of EC to prevent unintended pregnancy.