The paper discusses several issues related to the formation of new Lithuanian urban practice and theory in the rapidly developing urban environment. Resulting urban mutations and urban implications with problematic areas of contemporary cities are discussed. The authors identify the issues of undetermined and officially unacknowledged aspects and consequences, such as urban mutations, transformations and urban blight, by the inflexible Lithuanian urban planning system. The issue of inertia, lack of ability to adapt to a rapidly changing need of urban, economic fluctuations, and social change of organized development and planning are discussed.