In man and domestic animals, the ophthalmic exam is often a useful indicator of systemic disease problems as well as being important in determining the etiology of primary eye disease. However, in fish, the ophthalmic exam has not been a routine part of the clinical examination. The investigation of ophthalmic diseases in fishes has traditionally been limited to clinical observations of the anterior segment and microscopic evaluation of fixed tissue sections. However, a more comprehensive battery of diagnostic tests can provide important insights into the pathogenesis of eye disease in fishes. All of these procedures can be performed either with or without sedation.

The eye examination can be arbitrarily divided into three steps including history, clinical examination and necropsy.

In the history, especially important considerations include previous trauma from capture or aggression by tankmates, previous infection by bacterial or viral diseases and diet. A number of ophthalmic diseases have been associated with improper or deficient diets, including deficiencies in B vitamins, zinc or amino acids such as methionine.

The clinical examination should begin with a visual examination of behavior. Blind fish often become less aggressive or less territorial. The melanin pigmentation in fish is under neuroendocrine control and thus blind fish, lacking any visual input to the brain, are often dark. Exophthalmia commonly known as "pop-eye", is often a sequelae to systemic problems including viruses (e.g., channel catfish virus disease), bacteria (e.g., enteric redmouth disease), or gas emboli ("gas bubble disease").

The anterior segment exam includes the cornea, anterior chamber and lens. Visualization and localization of lesions in these structures is facilitated by using the slit-lamp biomicroscope. Corneal damage is common in display animals. The etiology in many cases is unknown. Cataracts are also common.

The posterior segment exam includes the vitreous and retina. There is little information on either normal or abnormal fundiscopic anatomy in fishes. Piscine eyes are adapted to vision in a fluid medium; thus, when removed from water, it is not possible to visualize the fundus without a strongly negative deopter system. This can be circumvented by immersing the fish under a thin layer of water while performing direct ophthalmoscopy, however, this is cumbersome due to the very short working distance for focusing on the eye. A more convenient approach is to use indirect ophthalmoscopy, which produces a much larger view of the fundus, allows a more rapid examination, and alleviate the need for immersing the eye in water. Another technique that can be used to evaluate retinal problems is electroretinography, which measures the electrical impulses produced by the retina in response to light.

Finally, necropsy of selected individuals is often desirable, if possible. Eye tissues should be fixed rapidly since fish tissues autolyze quickly.