This is the second in a two-part review of diagnostic cytopathology in veterinary medicine. As in human medicine, cytopathology is a minimally invasive, rapid, and cost-effective diagnostic modality with broad utilization. In this second part, the diagnostic applications of cytology in respiratory, gastrointestinal, genitourinary, endocrine, ocular, and central nervous system tissues are discussed with a section describing fluid analysis in veterinary medicine. As noted in the previous manuscript, which characterized the cytology of the skin/subcutis, musculoskeletal, and lymphoid tissues, the interpretation of veterinary cytology samples must be undertaken with extensive knowledge of the breadth of animal species, including familiarity with the frequency and clinical progression of diseases, both of which can be influenced by species, breed, and husbandry conditions. Similar to part one, this review focuses on the most common domestic companion animal species (dog, cat, and horse) and highlights lesions that are either unique to veterinary species or have relevant correlates in people. The cytologic features and biological behavior of similar lesions are compared, and selected mechanisms of disease and ancillary diagnostics are reviewed when appropriate. Supporting figures illustrate a subset of lesions. While not an exhaustive archive of veterinary cytology, the goal is to give cytopathologists working in human medicine a general impression of correlates and unique entities in veterinary practice. Diagn. Cytopathol. 2014;42:544–552. © 2014 Wiley Periodicals, Inc.