Koi Diseases are broken down into a few categories, the following are the most common.

    Bacterial Koi Diseases
    Fin, Mouth & Tail rot. (Flexibacter Columnaris), Holes. (Aeromonas/Pseudomonas). Bacterial Gill Disease.

One of the prime causes of fish mortality is bacterial disease. With the exception of "Columaris" nearly all bacterial infections occur after another problem has occurred, stress is a prime factor with bacterial disease. Most are gram-negative organisms. For a complete article on Flexibacter Columnaris click here
See Medicines for appropriate treatment.

    Fungal Koi Diseases

Are a secondary infection in the area of some other fish injury. Also affects damaged or disturbed fish eggs. Characterized by cottony or thick slimy patches anywhere on the fish. It spreads extremely rapidly without treatment. 
See Medicines for appropriate treatment.

    Parasitic Koi Diseases
Anchor worm, Fish lice (Argulus), Flukes, Leeches, Internal parasites.

Most fish carry parasites, but older fish develop a degree of resistance that prevents problems. Parasites like anchor worms and fish lice usually are a problem whenever present. Young fish are more susceptible to illness caused by parasites. Stress situations and seasonal climatic variations can bring on infections.
See Medicines for appropriate treatment.

Protozoan Diseases (also called parasites)
Chilodonella, Costia, Ich, Epistylis, Trichodina, to name the most common in Koi.
Protozoans are any of a large group of single-celled, usually microscopic, eukaryotic organisms, such as amoebas, ciliates, flagellates, and sporozoans. They are naturally occurring in waters when the balance and or parameters go out of wack. That is why water quality is so essential.

    Viral Koi Diseases

There seems to be very little in the way of effective treatments for viral infections like KHV or SVC. These two virus's will wipe out a pond in a matter of days. Usually by the time its detected its way to late. The best way to avoid these is to know where you purchase your fish and quarantine them for 2 weeks before introducing them into your main pond.  The only treatment that is somewhat effective is to heat the Koi up to a temperature of about 80 degrees than treat secondary infections. 
See Medicines for appropriate treatment.