Using data from the Second Regional Comparative and Explanatory Study (SERCE) conducted by UNESCO in Latin America, this paper investigates the association between gender and achievement in math's and reading in Primary Education (gender effect). So, the effect of socioeconomic status of the student and the school, and their interaction with gender inequality is studied, and the effect of gender variability among participating countries is also analyzed, for which bivariate multilevel models are used. The results show that children performed significantly better in math, while girls score higher on reading, even when socioeconomic status is "controlled". Regarding to the size of these gender gaps, it is noted that varies from country to country, with greater intensity than in developed countries. On the one hand, countries with high disparity in math also have high inequality in reading. In addition, girls are more affected than boys by the socioeconomic conditions. In the case of reading, the situation is different according to the sociocultural context of the school. These empirical results suggest that gender issues in school learning should be included in the political agenda of the countries of Latin America.