Abstract Objective To identify the trend in self-rated health in Spain by autonomous communities (AC) in the period 2001-2012, as well as differences by gender and age, and the influence of educational level. Methods A cross sectional study was carried out using data from the National Health Surveys from 2001 to 2011-12 and the 2009 European Survey. A descriptive analysis was conducted that included gender, age, educational level, and the AC of residence. Logistic regression analyses were developed to explore the temporal trend and the association between educational level and self-rated health. The predictive capacity of the model was calculated using the C statistic. Results The prevalence of low self-rated health was higher in women with low educational level. Self-rated health improved in women with high educational level (2001:18.6% vs. 2012:14.6%). The highest prevalence of low self-rated health was observed in Andalusia, the Canary Islands, Galicia and Murcia, with differences by gender. Low educational level was associated with low self-rated health in most AC, with good predictive capacity. In all AC except Asturias, low self-rated health was more frequent in women than in men. In Spain, the prevalence of self-rated health showed no variations in the period analyzed and improved in the Balearic Islands, Catalonia, and Madrid. Conclusions The prevalence of self-rated health in Spain differed by AC. Although health was unchanged during the period considered, inequalities were found in its temporal trend by educational level and gender, which could lead to an increase in health inequalities in women according educational level.