A Bit Different Chicks Eggs Genetics Hatching

Hatching Egg Fails

The Things That Can, & Do, Go Wrong

If you’ve been following my blog you’ll know I’ve got more than enough experience hatching with broody hens. That’s my preference because I think hens do the best job hatching and raising chicks. There’s still work on my part, but nothing like if I was doing it solo. Even with hen hatches, I’ve run into a number of issues and had to trouble-shoot chicks requiring assistance.

I have virtually no experience with incubator hatches: I’ve borrowed one in a pinch to save incubated eggs that have been abandoned by hens. I also donate eggs to elementary schools for their classroom hatches and know some of the issues they’ve dealt with.

In this piece I’ll explore various factors that impact the viability of hatching eggs. In a follow-up article I’ll talk about issues specific to incubator hatches.

For the last four years I’ve sold hatching eggs. I’m careful to select what I feel are the most viable: those with a uniform shape; no double-yolkers (twins rarely hatch) or thin shells; a defined wider end where the air sac is located; are unsoiled; and freshly laid. I store them at room temperature in an egg carton, pointed side down and tilt the box daily to ensure the embryo doesn’t stick to the membrane.

I don’t use eggs that have been washed, refrigerated or are older than four or five days. It’s also advisable to select eggs from hens that are at least a year old for a couple of reasons: pullets eggs are smaller and likely to produce small chicks; and you’re more likely to know if your layers are carrying transmittable pathogens as they get older.

There are eggs that appear perfect on the outside, but might be harbouring invisible issues on the inside that will affect their viability. You need to start with healthy breeding stock which are the product of good husbandry practices and appropriate diet so that both parents will produce viable, robust offspring. If there are issues with the parents their chicks may have minor health issues, serious deformities or not make it to hatch.

Here’s an overview of some of the issues resulting in chick deformities and mortality.

Drug or Toxin Residue

Always hatch eggs from healthy hens; don’t use eggs from sick birds or those on medications. Certain drugs and toxins can interfere with embryo development:

Tetracycline (antibiotic): skeletal malformation and erosion of the long-bone cartilage.

Sulfanilamide (antifungal): retarded growth, shortened long bones, abnormal extremities, parrot beak and rumplessness.

Penicillin (antibiotic): edema and hemorrhage in the wings, head and legs.

Aflatoxin B1 (mycotoxin): stunted growth; small liver and high chick mortality.


Infectious Bronchitis: stunting; retarded lung development; small hearts and enlarged spleens. Small chicks can hatch as a result of poor eggshell quality, thin shells and excessively porous shells, which causes excessive loss from the egg.

Newcastle Disease: reduced growth; small amniotic sac; abnormalities in neural and sensory tissues in early embryo development.

Botulism: muscle atrophy; fat accumulation; short upper beaks and joint problems.

Short Upper Beak
Short Upper Beak (Credit: Lisa Robbins)

Staphylococcus: extensive hemorrhage in the synovial lining of the joints.

E.coli:  high embryo mortality.

Aspergillus (fungus): Embryos are dark, or red and dwarfed.

Salmonella: (S. pullorum, S. gallinarum and S. Typhimurium) transmitted from the hen via the egg and can cause embryonic septicemia; high embryonic and chick mortality.

Vitamin Deficiency Diseases

Nutritional Deficiencies

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:

(‘day’ refers to the number of days of incubation)

Vitamin A: Death usually occurs @ day 2-3 from abnormalities in the circulatory system; abnormalities of kidneys and skeleton (i.e. skull and spinal column). Chicks hatched may have watery discharge from eyes or eyelids stuck together.

Incomplete Skull, Neural Tube Defect
Incomplete Skull, Neural Tube Defect (Credit: Lisa Robbins)

Vitamin B1 (Thiamine): High embryonic mortality during early stages of incubation and again at hatch; born without eyes; issues with peripheral nerves in chicks.

Chick Born Without Eyes
Chick Born Without Eyes

Vitamin B2 (Riboflavin): Deaths occur @day 3-5 days, 14 and 20-21; stunted growth; abnormal feathering; curled toes; spraddle leg; circulatory system issues; anemia; brown or dark green liver.

Vitamin B3 (Niacin): Decreased growth and development of skeletal muscles; edema; short upper beaks; nervous and vascular system abnormalities. Mortality peaks @ day 8-14.

Vitamin B5 (Pantothenic acid): Deaths @ day 2-4 or 14; subcutaneous hemorrhages; poor feathering; twisted legs and fatty livers.

 Vitamin B6 (Pyridoxine): Decreased embryonic growth; mortality peak @ day 8-14.

B6 Deficiency

Vitamin B7 (Biotin): High death rate @ day 3-4 or 17-21; parrot beak; skeletal deformities (underdeveloped long bones); hemorrhage; webbed toes; slipped tendon.

Vitamin B9 (Folic acid): Mortality @ day 20; appear normal, but many have bent leg bones; fused toes and beak malformations.

Vitamin B12: Mortality @ day 16-18; atrophy of legs; edema; hemorrhaging; fatty organs; head between legs malposition.

Vitamin D: Death @ day 18 or 19; with malposition in the egg; soft bones/poor skeletal development; rickets; prominent upper beak.

Malpositioned Chick (Small End of Egg)
Malpositioned Chick (Small End of Egg)

Vitamin E: Early death @2-5 days of incubation; hemorrhaging and circulatory failure (implicated with selenium); eye abnormalities; edema of neck and feet. Chicks have muscle weakness and wry neck.

Chick with Wry Neck
Chick with Wry Neck

Vitamin K: Hemorrhages in embryo and membranes, especially near or during hatch.

Calcium: The effects are more indirect, through poor egg shell quality, causing increased moisture loss and increased risk of contamination. Deficiency will cause stunted growth and skeletal development; embryo abnormalities.

Copper: Blood and circulatory defects; peak mortality day 3.

Fat/fatty acids: Slow development; embryo with head over right wing malposition in the egg; mortality day 1-4, 8-14 and 21.

Iodine: Late hatch; small thyroid; incomplete abdominal closure.

Iron: Low red blood cells and hemoglobin; poor embryonic circulation in candled eggs.

Manganese: Death prior to hatch; dwarfism; head malformations; edema; abnormal feathering; slipped tendon.

Phosphorus: Abnormal bone development; stunted growth; mortality day 14-16.

Protein, amino acids: incorrect beak development; protrusions in the brain; exposed viscera; twisted or shortened limbs; twisted spine; degeneration of the eye.

Exposed Viscera
Exposed Viscera (Credit: Lisa Robbins)

Zinc: Deaths prior to hatch; hatched chicks are weak; rumplessness; abnormal spinal column; underdeveloped eyes; missing limbs.

We are able to adjust our birds’ inputs (e.g. feed, medications), but there are some things we have no control over and that’s their genetic makeup. Obviously you don’t want to have inbred birds, but there are many genes that your birds may carry that are not expressed (visible). Often we don’t know what they are until those issues show up in subsequent generations. Pull birds with potential hereditary conditions from your breeding pool: wry tail, cross beak, and wry neck.

Crossbeak Embryo
Crossbeak Embryo (Credit: Randi Leigh)

If you have high hatch rates resulting in healthy robust chicks, then this piece probably doesn’t apply to you. But if you are experiencing any issues with hatching or chicks, whether a one-off or consistently, start paying attention to the factors that might be affecting their viability.

  • Is your breeding stock healthy?
  • Are a high percentage of your eggs fertilized?
  • Are the eggs viable, but don’t hatch?
  • When are the embryos dying?
  • Do you have chicks hatch with birth defects or fail to thrive?

If you’re curious, do an ‘eggtopsy’: crack open unhatched eggs once you’re past the expected hatch date to see if they were: fertilized or not; have embryos that died and even so, when; or contain fully developed chicks that didn’t make it out of the egg.

Check for any obvious issues: undeveloped or absent eyes; abnormal beak; malposition in the egg; anatomical abnormalities (misshapen skull, extra legs). These details are clues as to what might have gone wrong and how to remedy them.

Reference: Hatchability Problem Analysis, University of Florida, author H.R. Wilson. Read more here.

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