Neonatal reptiles may develop problems.  If an egg is disturbed during its incubation, the reptile may hatch too early.  If the incubator has unsanitary conditions, such as spoiled eggs, mold, and foul smells, the baby may quickly develop an infection.  Sometimes babies are born weak, either due to a malnourished mother or a bad incubation environment (e.g., too hot, too cool, too wet, too dry, not enought oxygen).  Babies that are the result of hybridization between different species, and sometimes even different subspecies, are more likely to have problems than "pure" breedings.

It can be difficult to distinguish between a problem hatchling and a “shy” hatchling.  If a pipping egg has a foul or sweet smell, or the fluid is anything other than clear and colorless, there's a problem.  A recently pipped hatchling may not have fully absorbed its yolk before leaving the egg.  If this yolk sac is a uniform shiny yellow (like the yolk of a fresh chicken egg) then it is healthy.  If it is dull, tan or brown, or has a smell, it is probably infected.  If a recently hatched baby has alread absorbed its yolk  but there is a firm mass palpable in the body, it may have an infected yolk sac and is an indication to intervene.  Unfortunately at this point many baby reptiles are riddled with bacteria and may not survive.

Potential problems with live-bearing (viviparous) reptiles are similar.  If the “birth sac” has discolored membranes, or a foul or sweet smell, the newborn is heavily contaminated with pathogenic bacteria or fungi.  The most common signs of a newborn snake with a retained yolk sac is failure to shed successfully, failure to eat, or detection of a firm mass in its abdomen.  Maternal and paternal behavior can suggest a problem in some viviparous lizards, such as the prehensile-tailed skink Corucia zebrata.  In every case where there has been a problem with the yolk sac, the baby is not attended by the parents and is often found visible in the enclosure rather than hiding.  If the yolk sac is not removed, the skink becomes dehydrated, its skin roughens and discolors, and a septic blush quickly develops.

Surgical intervention is needed to treat baby reptiles with infected yolk sacs.  It's not enough to remove the yolk you see outside the body since the majority of it is inside the baby's body. There are few contraindications to this surgery, known as an omphalectomy.  If the surgery is performed as soon as possible, typically within 24 hrs of birth, most babies survive. 

Anytime a neonatal reptile has a problem such as retained yolk sac it warrants a review of the husbandry and nutrition of the parents to minimize risk of future offspring with problems.