The two sides agreed the initial link-up when Regini spent two years on loan at Empoli, but he managed to break into the first team at the Luigi Ferraris last season.
After impressing coach Sinisa Mihajlovic, Samp have moved to secure his future on a permanent basis ahead of 2014-15.
"I am very happy," Regini told the club's official website.
"My team-mates and I coped very well (last season) and since November we speak clearly in his (Mihajlovic) favour.
"There were months when we did the important things together (last season) and I honestly cannot wait to get back to work in order to continue working."
Regini made 31 appearances in all competitions last season as Sampdoria recovered from a disappointing start to claim 12th place in Serie A.
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