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In a traditional SQL Server cluster when failover occurs, all clients that are connected to the SQL Server failed instance lose connections and each client must re-establish a new connection to failover cluster instance.

Does AlwaysON Availability Group mitigate this problem? Is failover in case of SQL Server 2012 AlwaysON availability group transparent to clients connecting to the SQL Server?

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No. During a failover, clients will notice. Your connection to the SQL Server will be broken, and you'll have to retry your transaction.

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For those reading this post later as a result of a web search. It is indeeded described in SQL Server BOL here. Doh... I could not find it earlier....

Behavior of Client Connections on Failover

When an availability group failover occurs, existing persistent connections to the availability group are terminated and the client must establish a new connection in order to continue working with the same primary database or read-only secondary database. While a failover is occurring on the server side, connectivity to the availability group may fail, forcing the client application to retry connecting until the primary is brought fully back online.

If the availability group comes back online during a client application’s connection attempt but before the connect timeout period, the client driver may successfully connect during one of its internal retry attempts and no error will be surfaced to the application in this case.

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