The immunization of an animal with a whole proteome or the infection of an animal and the screening of the resulting antibody repertoire on either the same or different proteome(s) or the infecting agent(s), omits the laborious steps of recombinant protein expression and purification to obtain multiple antigen binders. This procedure allows the identification of antibodies that are specific to unique or common signatures of different proteomes without prior knowledge of these signatures.Nanobodies are the smallest (15 kDa, 2.2 nm diameter, 4 nm height) in vivo affinity-matured functional antigen-binding entities that are derived from camelid heavy-chain antibodies. Due to their small size, recognition of unique epitopes, high affinity, and easy tailoring, nanobodies are attractive affinity reagents for various applications, including diagnosis and therapy.We detail a protocol to generate, isolate, express, and purify anti-infectome/anti-proteome nanobodies.