All fish hatcheries have a rating indicating their disease status. In the Great Lakes Basin, the protocol for assigning disease status is coordinated by the Great Lakes Fishery Commission. This rating is used to classify a facility as disease free or to alert others of possible or known disease exposure at that facility. In order to be classified as disease free, a hatchery must be inspected three times over a two-year period and show no incidence of disease. Three of Michigan's hatcheries, Thompson, Platte River, and Wolf Lake, rely on wild fish for egg sources. Consequently, these hatcheries do not have the possibility of a disease-free status. Oden and Harrietta State Fish Hatcheries are currently disease-free and Marquette State Fish Hatchery is working on getting re-classified as disease-free. Michigan also has strict regulations controlling the import of fish from outside the Great Lakes watershed to prevent non-native disease agents from being introduced to the Great Lakes watershed.

Occasionally anglers catch fish with black, pinhead size spots which cause the fish to have a peppered appearance, or a fish may be caught which has white to yellow colored grubs under the skin of in the flesh. Yellow perch taken from the shallower waters of the Great Lakes often contain red worms coiled within the body cavity. All these conditions are caused by common fish parasites. Fish with these parasites are safe to eat, as all these (and any other parasites) are killed by cooking. Black Spot and yellow grub parasites are most common in bass, sunfish (all species), and northern pike, and red worm is specific to yellow perch. These and related parasites may be found in other species of fish as well.

It is not unusual for anglers to catch walleye with pink, whitish, or yellowish wart-like growths on their bodies and fins. These are caused by fish viruses, the most common of which is called lymphocystis. This is primarily a skin disease, and the flesh is usually not affected. Lymphocystis is harmless to humans and affected fish are safe to eat. Skinning the fish usually removes all diseased tissue. If a legal size fish is heavily affected and appears aesthetically unpleasing, it should be kept for disposal because a fish that is released will only spread more virus.

Northern pike from some waters are occasionally caught with various size and colors of external tumors which may be whitish, creamy, pink, or red. In advanced stages, the tumors are ugly open sores tinged with red and are often referred to as red sore. These tumors are caused by a naturally occurring virus which is specific to northern pike and muskellunge. The disease is not known to be infectious to other animals or man; however, affected fish are not aesthetically pleasing and should not be eaten. Affected fish (of legal size) should be kept for disposal because a fish that is released will only serve to spread the infection to other fish.