Ocular cytology specimens are small, with limited options for a repeat biopsy. Appropriate handling of these specimens and triaging for ancillary testing can be taxing. In this article, the author reviews a selection of potentially challenging diagnoses and current common practices and methods used in diagnosing ocular diseases by cytology. The majority of cytology specimens submitted for evaluation of ocular diseases can be divided into 3 major categories: surface epithelial corneal and conjunctival cytology samples, intraocular fluids from the anterior (aqueous fluid) or posterior (vitreous fluid) chambers of the eye, and intraocular fine-needle aspiration specimens. The clinical findings, testing, and cytologic features of ocular surface epithelial infections, inflammations and neoplasia are discussed; and challenges in processing and diagnosing intraocular infections, chronic uveitis, and vitreoretinal lymphoma are reviewed. Novel molecular testing in the cytologic diagnosis and classification of uveal melanoma also is explored. Cytology evaluation of corneal epithelial and stromal cells, anterior chamber and vitreous samples, and fine-needle aspiration biopsies can provide detailed diagnostic findings to aid in the treatment and follow-up of patients with ocular diseases.