Vaccine efficacy can be enhanced by delivery of antigens in synthetic microspheres. The process of antigen incorporation into microspheres can expose fragile antigens to damaging conditions, such as high temperatures, and to bacterial contamination. Maintenance of immunogenicity of several antigens and reduction of bacterial load in alginate microspheres following boiling was evaluated. Mice were immunized subcutaneously, initially and again 21 days later, with either non-boiled or boiled microspheres containing ovalbumin (OVA), a culture supernatant vaccine of Pasteurella haemolytica (PHV), or a potassium thiocyanate extract of P. multocida (PTE). Serum samples were obtained prior to immunization and at the time of euthanasia 28 days later. Culture of microspheres showed that boiling completely eliminated aerobic bacterial growth for OVA-containing microspheres, and reduced growth by a factor of 104 for PTE microspheres. More bacteria were cultured after boiling than before for PHV microspheres. ELISA performed on serum and intestinal lamina propria explant supernatants showed that immunogenicity of PHV microspheres was not altered by boiling. Boiled OVA microspheres were still able to stimulate a significant serum IgG anti-OVA titer in mice, but boiled PTE microspheres completely lacked immunogenicity. Elispot assays of spleens showed that only PHV microspheres were able to retain immunogenicity after boiling. Results indicate that boiling is not an effective means for reducing the bacterial load of alginate microspheres and that the process is associated with a diminution of vaccine immunogenicity.