The article examines methodological approaches to economic crises, gives a characteristic of crisis phenomena in economy. The reasons for the development of crisis in agriculture are considered and prerequisites for overcoming it are systematized. The factors of increasing instability of agricultural sector in the context of global economic crisis are analyzed. A number of circumstances are highlighted that determine its negative and positive effects, without which it is difficult to objectively determine the probable losses and predict potential options for the development of domestic agro-industrial complex. Particular attention is paid to structural crisis. The authors conclude that current situation in agricultural sphere does not fall under the traditional classification of economic crisis processes and propose to supplement the methodology of assessing periodic crises by including a systemic crisis. The methodological foundations for diag- nosis of crisis situations in AIC of Kazakhstan have been developed, which represent a set of methods and techniques that allow to determine and study anxiety states in it in order to prevent in the future. The methodology outlines conceptual approaches to assessing crisis conditions of economic systems at sectoral and economic levels. The diagnosis of crisis phenomena is carried out on the basis of comparing critical values of indicators characterizing economic development with their actual values, followed by calculation of integral coefficient of the level of agro-industrial production in the republic.