Coccidiosis, a single celled parasite that attaches and infests lining of the gut wall, in turn causing malabsorbtion of nutrients. It also prevents the gut from reabsorbing water, resulting in diarrhea.
Coccidial infestation can result in serious disease, with the significant loss of water and mineral salts in diarrhea making the bird prone to opportunistic infections (low immune response)
Nearly all pigeons have some degree of Coccidial infection, but when the numbers get out of control, it's serious.
Oocysts (Coccidia eggs) may lay dormant in soil or droppings for some time.
Environmental hygiene is key in the control of disease.
Treatments: Amprolium (Coxoid); Clazuril (Appertex) are available over the counter (follow directions) and yes, treat prior to breeding.
Another possibility: Helminthiasis (Parasitic Worm)
There are four parasitic worms affecting pigeons: Tapeworms are not very common, nor are gapeworms, but they are nonetheless possible; roundworms and hairworms are others we see more of.
There are a variety of wormers available Piperazine (Biozine) for roundworms; Levamisole (Spartakon); Fenbentyl (Panacur) and Avicas. Ivermectin, which has the additional advantage of controlling Ectoparasites (parasites on the birds, not just in them) as well as worms.
Good luck,
Certified Avian Specialist
Cert. Avian Specialist; Int. Assoc.Animal Behavior Consult; Pet Ind. Joint Advisory Council; author