The aim of this study was to analyze inequalities in the prevalence of poor mental health and their association with socioeconomic variables and with the care network in the Autonomous Communities in Spain. A cross-sectional multilevel study was performed, which analyzed individual data from the National Health Survey in Spain (ENS), in 2006 (n = 29,476 people over the age of 16). The prevalence of poor mental health was the dependent variable, measured by the General Health Questionnaire (GHQ-12 > = 3). Individual and contextual socioeconomic variables, along with mental health services in the Autonomous Communities, were included as independent variables. Models of multilevel logistic regression were used, and odds ratios (OR) were obtained, with confidence intervals (CI) of 95%. The results showed that there are inequalities in the prevalence of poor mental health in Spain, associated to contextual variables, such as unemployment rate (men OR 1.04 CI 1.01–1.07; women OR 1.02 CI 1.00–1.05). On the other hand, it was observed that inequalities in the mental health care resources in the Autonomous Communities also have an impact on poor mental health.