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 or 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.