Causes of deformities and embryo mortality - the hatching egg

You cannot hatch a perfect chick from an imperfect egg. It's just not going to happen. To get a perfect egg, you need to start with good husbandry practices and continue with correct feeding, supplying the building blocks needed by the hen to produce an egg that will in turn provide everything needed by the developing embryo to grow into a perfect, complete baby chicken. If something is missing or done incorrectly, there is going to be problems. These problems range from minor oddities, to serious deformities and losses and it can so easily be prevented. This article will break down the causes of chick deformities and mortality starting with...

Breeder diseases and drugs/toxins residue in eggs

Do NOT incubate eggs from sick hens. Tempting as it may be in some cases, wait until the hen is well again and wait out the withdrawal period of any drugs given to the hen to treat her. **Certain drugs do not leave a residue and certain drugs do not have a noticeable effect on the embryo, but it's a gamble and the stakes are high. Certain drugs and toxins can wreak havoc with embryo development though such as:

Tetracyclines which causes inhibition of mineralsation of the embryo's skeleton, erosion of the long-bone cartilage and therefore skeletal malformations.
Sulfanilamide which causes retarded growth, shortened long bones, extreme micromelia, parrot beak and rumplessness.
Penicillin which causes edema and hemorrhage in the wings, head and legs.
Aflatoxin B1 which causes stunting (starting around day 12), small liver and high chick mortality.
Ammonia (if used in incubators) results in failure of neural tube to close and embryo/chick mortality.

Diseases and certain micro-organisms can have equally devastating effects:

Infectious bronchitis causes stunting, retarded lung development, small hearts and enlarged spleens. Small chicks can hatch as a result of poor egg shell quality, thin shells and excessively porous shells, which in turn causes excessive moisture loss from the egg.
Newcastle disease causes reduced growth, small amnion, as well as abnormalities in neural and sensory tissues in early embryo development.
Botulism causes muscle athropy, fat accumulation, short upper beaks and joint problems.
Staphylococcus causes extensive haemorrhage and tissue damage.
Stretococcus causes destruction of the senovial lining of the joints.
E.coli causes rots.
Aspergillus causes black or dark green rots. Embryos are dark, or red and dwarfed.
S. pullorum, S. gallinarum and S. Typhimurium are transmitted via the egg. They cause embryonic septicaemia and high embryonic and chick mortality.

Nutritional deficiencies in hatching eggs

Developing embryos need a range of nutrients in adequate and correct amounts in order to develop and grow at the required rate. Shortages and in some cases an excess of the necessary nutrients can cause deformities and embryo deaths. Here is a breakdown of the different nutrients and the effect incorrect levels have:

Vitamin A - Death usually occurs at about 48-72 hours of incubation from abnormalities in the circulatory system. Shortages cause abnormalities of kidneys and a great excess causes skeleton abnormalities, especially in the skull and spinal column. Chicks hatched may have watery discharge from eyes or eyelids stuck together.
Vitamin D - Death at about 18 or 19 days of incubation, with malpositions, soft bones/poor skeletal development, rickets and with a defective upper beak often prominent.
Vitamin E - Early death at about 84 to 96 hours of incubation, with hemorrhaging and circulatory failure (implicated with selenium), eye abnormalities, edema of neck and feet. Chicks hatching will show signs of muscle weakness.
Thiamin - High embryonic mortality during early stages of incubation and again at hatch, but no obvious symptoms other than polyneuritis in those that survive.
Vitamin K - Haemorrhages in embryo and membranes, especially near or during hatch.
Riboflavin (Vitamin B2) - Deaths occur at 60 hours, 14 days, and 20-21 days of incubation, with most deaths early if deficiency becomes severe. Depletion of the supply of this vitamin can result in stunted growth, clubbed down, curled toes, and disorganised circulatory systems.
Niacin - Decreased growth and development of skeletal muscles, edema, short upper beaks and nervous and vascular system abnormalities.
Biotin - High death rate at 19 days to 21 days of incubation, parrot beak, chondrodystrophy, several skeletal deformities such as under developed long bones, haemorrhage in the embryo and webbing between the toes.
Pantothenic acid - Deaths around days 2-4 and again around day 14 of incubation, although marginal levels may delay problems until hatch. Subcutaneous haemorrhages, poor feathering, twisted legs and fatty livers.
Folic acid - Mortality at about 20 days of incubation. The dead generally appear normal, but many have bent tibiotarsus (long leg bone), syndactyly (fused toes) and beak malformations. In poults, mortality at 26 days to 28 days of incubation with abnormalities of extremities and circulatory system.
Vitamin B12 - Mortality at about 20 days of incubation, with atrophy of legs, edema, hemorrhaging, fatty organs, and head between thighs malposition.
Manganese - Deaths peak prior to emergence. Chondrodystrophy, dwarfism, long bone shortening, head malformations, edema, and abnormal feathering are prominent. Perosis.
Zinc - Deaths prior to emergence, and the appearance of rumplessness, depletion of vertebral column, eyes underdeveloped and limbs missing.
Iodine - Prolongation of hatching time, reduced thyroid size, and incomplete abdominal closure.
Iron - Low hematocrit; low blood hemoglobin; poor extra-embryonic circulation in candled eggs.

Protein, amino acids - Deficiency, imbalance or excess of some amino acids can cause abnormalities such as incorrect beak development, disorganised protrusions in the brain, exposed viscera, twisted and shortened limbs, twisted spine and degeneration of the eye.
Calcium - The effects are more indirect, through poor egg shell quality, causing increased moisture loss and increased risk of contamination. Shortages will cause stunted growth and skeletal development and a great excess will also cause embryo abnormalities.

Suggested and further reading:
Egg failure to hatch - Diagnosing incubation problems (Article)
Emergencies / Diseases / Injuries and Cures (Forum section)
Feeding & Watering Your Flock (Forum section)​