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All recombinant vaccines fall into three fundamental classes namely, live genetically modified, recombinant inactivated, and genetic vaccines.

Live genetically modified vaccines can be bacteria or viruses, generally with two or more genes inactivated or deleted. They can also be vaccines carrying a foreign gene from a different disease agent, referred to as vaccine vectors. These vaccines are developed to attenuate the infectious agent. An additional recent technique of creating a live genetically modified vaccine is to utilize an infectious clone of the disease causing agent. An infectious clone is produced by isolating the complete genome of the disease agent in the lab. This isolated or cloned genome can be purposefully and specifically altered in the lab and then utilized to re-create the live genetically modified organism.

Recombinant inactivated vaccines are the subunit vaccines consisting of only a part of the entire organism. Subunit vaccines can be synthetic peptides produced in the lab. It can also be whole proteins extracted from the disease agent or the one that is expressed from the cloned genes. Numerous systems can be utilized to express a recombinant protein and the expression systems can be cell free or use entire cells. The expression systems that use entire cells includes prokaryotic such as Escherichia coli (bacteria based) and eukaryotic such as yeast, mammalian, avian or insect based systems. An additional type of recombinant subunit vaccines, referred to as virus-like particles or VLPs, can be generated when one or more cloned genes that characterize the structural proteins of a virus are expressed at the same time and self-assemble to form VLPs.

Genetic or DNA vaccines are generally plasmids, which contain a foreign gene from an infectious agent and a promoter to initiate its expression in the target animal. These plasmids can be maintained in bacteria such as E. coli .The plasmids are purified from the bacteria and the DNA is injected directly into the animal by intramuscular means or into the skin. The cells of the animal take up the naked DNA, and as a result the immune response is induced to the protein that is expressed from the foreign gene.