Parasites are a real health issue when it comes to koi fish. The most common way koi fish contact parasites is from other fish. Before a new koi is introduced to the pond, it is extremely important that the new fish be quarantined for 3 weeks.
During this time period the koi should be treated for parasites. Isolating a koi for 3 weeks in a quarantine tank, without treating the koi, is no assurance that the koi is parasite free. All that tells you is that if it has parasites, there are not enough of them to make it sick at this time. If you do not have a separate quarantine tank in which to treat a new koi in, then be very careful who you purchase your new koi from.
The five most common parasites that affect koi fish are: flukes, costia, chilodinella, trichodina and ich. All of these parasites are microscopic which means you cannot see them without the aid of a microscope.