There is great interest in identifying and modelling real estate market bubbles over time. However, the spatial dimension of those bubbles gets less attention. While building on the theory of real estate market equilibrium and formation of market bubbles, this research focuses on the spatial bubbles of the market value of apartments inside a city. This approach adds another dimension to the phenomena of real estate market bubbles. The scientific problem of this study is whether the spatial differentiation of real estate encourages the formation of spatial bubbles in real estate market. The object of research is the spatial bubbles in real estate market. The aim of research is to identify the impact of spatial bubbles on real estate market value. Because of the nature of real estate market, the supply and demand of real estate does not match, therefore real estate almost never reaches the equilibrium market value and bubbles appear. The main idea behind this research is that the supply and demand equilibrium model can be applied not only to the changes over time but also across space inside a city. The spatial bubbles appear because of unexplained variance. The empirical research focuses on unexplained variance across space of market value of homogeneous apartments in two major cities in Lithuania. The prominent variance is eliminated through careful selection of projects and control variables such as floor and size of an apartment, distance to civic points and location. Up to 39% of unexplained variance of apartment market value across space was found when looking at 3D diagrams of residualised apartment market value of the selected cities. The main reasons behind formation of those spatial bubbles should be addressed by further research for deeper understanding of the phenomenon of spatial bubble formation.