The two accused, Leutogi Te'o and Luse Emo Tuavale, entered a not guilty plea to manslaughter, conspiracy to defeat the course of justice and negligence.
The women remain on bail for a hearing set down for January next year.
The one year old infants died in July soon after receiving a vaccination for measles, mumps and rubella at a clinic in Savai'i.
A Commission of Inquiry into their deaths is set to start next Monday.