While comes to breeding, Budgies suffers difficulties for various reasons. If the adult budgies have some diseases, it will affect the chicks and lead it to die. Other female budgerigars may fight over the nest box, attacking each other or a brood. Sometimes male budgerigars are not interested in the opposite gender, and will not reproduce with them. Sometimes a flock setting, several pairs housed side by side, where they can see and hear each other are necessary to stimulate breeding. Another problem may be the birds' beak being under lapped. This is where the lower mandible is above the upper mandible.

Most health issues and physical abnormalities in budgerigars are genetic. Care should be taken that birds used for breeding are active, healthy, and unrelated. Budgerigars that are related or who have fatty tumors or other potentially genetic health problems should not be allowed to breed. Parasites (lice, mites, worms) and pathogens (bacteria, fungi and viruses), are infectious micro organisms and thus transmitted between individuals through either direct or indirect contact. Nest boxes should be cleaned between uses.

Splay leg, a relatively common problem in baby budgerigars , in which one of the budgerigar's legs is bent outward, preventing it from being able to stand properly and compete with the other chicks for food and can also lead to difficulties in reproducing in adulthood, results from young budgerigars slipping repeatedly on the floor of a nest box. It is easily avoided by placing a small quantity of safe bedding or wood shavings in the bottom of the nest box. Alternatively, several pieces of paper may be placed in the box for the female to chew into bedding.

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