Immunomagnetic cell separation has been shown to be a highly attractive alternative to density-dependent methods for islet purification. There are two types of beads, magnetic inducible microspheres (MIMS) and Dynabeads, in this context. The aim of this study was to compare the two beads and ligands using the same method of purification. Two batches of collagenase were used. Using either monoclonal antibodies or lectins with a specificity for rat acinar tissue, the beads were used to immunomagnetically label pancreatic digest before magnetic separation. The results showed that both MIMS coated with a lectin and Dynabeads coated with an antibody removed 80% of the acinar contamination with a 70% islet yield. However, the MIMS were significantly less effective with the second enzyme, which produced larger acinar particles. In this study, although the MIMS produced the least nonspecific islet trapping, the Dynabeads coated with Leicester Department of Surgery no. 10 antibody were found to be the most efficient particle for immunomagnetic islet purification.