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In the last year the automation systems in power substation start to rely on networks thanks to the introduction of the IEC 61850 standard. Besides, it generates a general interest on synchronization also in the field of substation automation systems. In fact, timestamping of critical events or synchrophasor measurements can have a great advantage from distributed synchronization protocols like IEEE 1588. This paper analyzes the current situation and proposes new architecture for the test of IEEE 1588 solutions before introduction in the market. The focus is mainly on compatibility with real existing systems and its goal is the performance comparison of different implementations. First experimental results on real substation automation system show a great cabling reduction and a simplified maintenance in the IEEE1588-based systems. On the other hand, the synchronization performance are slightly worse: the maximum time difference among clocks of the system is about 80 ns for IEEE1588 with respect to 15 ns of typical IRIG-B-based system.