Kalcineurin je heterodimer od 61-kD kalmodulin-vezujuće katalitičke podjedinice, kalcineurina A i 19-kD Ca2+-vezujuće regulatorne podjedinice, kalcineurina B. Postoje tri izozima katalitčke podjedinice, svaka od kojih je kodirana zasebnim genom (PPP3CA, PPP3CB, i PPP3CC) i dve regulatorne izoforme, takođe kodirane zasebnim genima (PPP3R1, PPP3R2).
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