We present the arguments for an urban agglomeration concept where urban agglomeration is considered as a complex and naturally shaped socio-economic system. The preconditions of shaping such agglomerations are identified as well as the criteria for their assessment. The conditions which enhance or hinder agglomeration processes are also described. On the base of the expert polling, we compare the opinions about positive and negative effects expected from agglomeration process. As an example, we show the negative impacts of the agglomeration which may take place due to attempts «from the top», i.e. those making by the Siberian regional authorities. We come to the conclusion that a natural course of any agglomeration process through inter-municipal cooperation would be more advisable.