This study is aimed to analyze the tendencies of agricultural pollution and their impact on the incidence rates of the rural population of the Republic of Kazakhstan. A retrospective assessment of statistical indicators of agricultural emissions of greenhouse gases and pesticide load, as well as a comparative analysis of the incidence rate ratios of the population of Kazakhstan and other countries, are chosen as the main research methods. The study shows that an increase in greenhouse gas emissions from livestock and crop production, the introduction of pesticides and other chemical plant protection products lead to an increase in morbidity and mortality. The high growth rates of registered congenital anomalies among the rural population, as well as the incidence of cerebrovascular diseases and asthma, are especially disturbing. After studying and summarizing expert opinions, two priority directions that could contribute to reducing the level of agricultural pollution in the Republic of Kazakhstan have been identified. Measures should be aimed at improving the mechanisms for the use of pesticides in crop production, as well as reducing greenhouse gas emissions in Kazakhstan’s agriculture.