While the phase angle of any of the bus voltages can be chosen as the angular reference in the state estimation formulation of positive sequence networks, the same approach does not readily extend to three-phase network state estimation problem. It is commonly assumed that there is at least one bus where the bus voltages are perfectly balanced with phase angles displaced ±120° and these balanced three phase voltages are used as the three-phase reference in solving the three-phase state estimation problem. This assumption may be quite realistic in transmission networks, and for distribution networks with a strong transmission system connection. However, it might not be realistic to assume existence of a perfectly balanced reference bus in today’s distribution systems with ever increasing penetration of renewable sources or for isolated operation of microgrids. In this paper, a novel state estimation formulation will be presented which facilitates correct solution irrespective of the existence of buses with perfectly balanced voltages. The new formulation is general, and lends itself to bad data processing. It yields accurate results in any three-phase power system irrespective of its operating conditions (balanced or highly unbalanced), configuration (isolated microgrid, connected to transmission system, etc.) and whether or not it contains any synchronous generators. The performance of the method is validated using the IEEE 123 bus three-phase system.