here's a great link with an excerpt below http://www.natureform.com/kb/index.php?article=1011 Troubleshooting: Specific Problems Sign: Not pipped. Full-term embryo, large yolk sac; yolk sac may not be fully enclosed by abdominal wall, may have residual albumen. Causes: Inadequate turning, resulting in decreased embryonic membrane development and nutrient absorption. Humidity too high during incubation or after transfer. Incubator temperature too low. Hatcher temperature too high. Eggs chilled (e.g., at transfer). Nutritional deficiencies. Heredity. Embryological development accident. Breeder diseases. Inadequate ventilation. Prolonged egg storage. Sign: Pipped. Full-term embryo, dead in shell. Causes: Low humidity or temperature for a prolonged period. Low humidity during hatching. High temperature during hatching. Nutritional deficiencies. Breeder diseases. Poor ventilation. Inadequate turning during first 12 days. Injury during transfer. Prolonged egg storage. Sign: Shell partially pipped, embryo alive or dead. Causes: See 8.a-i. Excessive fumigation during hatching. Eggs set small end up. Sign: Chicks hatch early; tendency to be thin and noisy. Causes: Small eggs. Differences among breeds. Incubator temperature too high. Incubator humidity too low. Sign: Chicks hatch late. Causes: Large eggs. Old breeders. Eggs stored too long (40 min. increase in incubation time/day of storage, .5% to 1.2% decrease in number hatched/day of storage). Incubator temperature too low. Weak embryos. Inbreeding. Incubator humidity too high. Sign: Slow, protracted (drawn-out) hatch. Causes: Mix in the incubator of eggs stored for long and short periods (1.2% loss of hatch/day of storage when all eggs set at the same time; only .5% loss/day when eggs stored for long periods are set earlier to allow a longer incubation period). Mix of eggs from young and old breeders. Mix of large and small eggs. Improper egg handling. Hot or cold spots in incubator or hatcher. Incubator or hatcher temperature too high or too low. Room ventilation system improper; high positive pressure or low negative pressure. Such pressures may alter incubator or hatcher ventilation. Sign: Trays not uniform in hatch or chick quality. Causes: Mix of large and small eggs. Mix of eggs from young and old breeders. Mix of eggs from different strains or breeds. Some eggs stored much longer. Lack of uniform ventilation in setter or hatcher. Disease or other stress in one or more breeder flocks. Variation in egg storage procedures among flocks. Sign: Sticky chicks; chicks smeared with albumen. Causes: Low incubation temperature. High incubation humidity. Improper turning. This results in reduced embryonic membrane growth and reduced nutrient absorption. Old eggs. Very large eggs. Sign: Chicks stuck in shell, dry; chicks with shell fragments stuck to down feathers. Causes: Humidity too low during egg storage, incubation, and/or hatching. Improper egg turning. Cracked eggs or poor shell quality. Sign: Premature hatching; bloody navels. Causes: Incubator and/or hatcher temperature too high. Sign: Small chicks. Causes: Small eggs. Low humidity during egg storage and/or incubation. High incubation temperature. High altitude. Hatcheries at high altitudes (>1,500 m or 4,920 ft) may need to adjust for low humidity, carbon dioxide, and oxygen. Atmospheric pressure <600 mmHg (~1,830 m or 6,004 ft) reduces growth and metabolic rate, increases loss of water from the egg. Thin, porous shells. Sign: Unhealed navel; dry, rough down feathers. Causes: High incubator temperature or wide fluctuations in temperature. Low temperature in hatcher. Humidity too high in hatcher or not lowered when hatching complete. Inadequate breeder nutrition. Sign: Unhealed navel, wet, odorous; mushy, large, soft-bodied, and lethargic chick. Causes: Omphalitis (navel infection). Contamination from dirty trays, unsanitary machines or hatchery, dirty eggs, inadequate egg sanitation or fumigation. Low incubator temperature. High incubator or hatcher humidity. Inadequate ventilation. Sign: Weak chicks. Causes: High hatcher temperature. Poor hatcher ventilation. Excessive fumigation. Contamination. Sign: Chicks malpositioned. Normal position after 19 days of incubation: embryo's long axis same as long axis of egg; head in large end of egg; head to the right and under right wing; beak toward air cell; feet toward head. Causes: Eggs set small end up or in horizontal position. Inadequate or improper turning. High or low incubator temperature. High humidity. Old breeders. Round-shaped eggs or very large eggs. Nutritional deficiencies, especially vitamin A and vitamin B12. Eggs handled or stored improperly. Retarded development. Embryos <18 days old may be in a position different from that for hatching but one normal for their age (for example, the head-between-thighs position). The feet-over-head position is hard to distinguish and may be normal. The beak-over-wing position is probably a normal variant. Some malpositions are lethal; others are not. Sign: Malformations. Causes: Improper egg storage. Jarring of eggs or transporting large end down. Heredity. Nutritional deficiencies, e.g., biotin, riboflavin, zinc, or manganese. Inadequate turning. Improper egg orientation, e.g., small end up. High or low incubator temperature. Breeder diseases. Inadequate ventilation or shells with low porosity or permeability. Sign: Crooked toes, spraddled legs. Causes: High or low incubator temperature. Inadequate nutrition. Smooth bottom hatching trays. Sign: Short down, wiry down. Causes: Nutritional deficiencies, especially riboflavin. Mycotoxins and other toxic or inhibitory substances, resulting in nutritional deficiencies. High incubation temperature during days 1 to 14. Sign: Eyes closed, down stuck to eyes. Causes: Temperature too high in hatcher. Humidity too low in hatcher. Down collectors inadequate. Chicks remain in hatcher too long after hatching Excessive air movement in hatcher. Sign: Exploders. Causes: Dirty eggs from nest. Dirty nests. Floor eggs. Eggs improperly washed; eggs wiped or cleaned with contaminated cloth or buffer. Dust from breeder house, cooler, transport, etc. Water condensation on eggs (sweating). Water sprayed, fogged, or splashed on eggs; eggs dipped in contaminated solutions. Contamination from earlier exploders, leakers, or broken eggs. Contamination from handling eggs with dirty hands or equipment. Contaminated setter flats, air filters, water (humidity) system. Sign: Dwarf embryos: runts in growing chicks. Causes: Egg contamination. Hatchery contamination, especially during hatching. Breeder diseases. Heredity. Nutritional deficiencies. Thyroid abnormalities. Sign: Crossed beak, twisted beak. Causes: Heredity. Sign: Missing eye(s), other eye abnormalities. Causes: High incubator temperature during days 1 to 6. Low oxygen during days 1 to 6.30. Sign: Exposed brain. Causes: High incubator temperature during days 1 to 3. Low oxygen during days 1 to 3. Sign: Red hocks in hatched chicks or unhatched pips. Causes: Prolonged pushing on shell during pipping and hatching. Vitamin deficiencies. Thick shells, as in pullet flocks. High incubator humidity and/or low incubator temperature. Sign: Small air cell, broad pip area, membrane incompletely cut, red hocks, edematous chick, unabsorbed albumen, yolk incompletely retracted, egg weight loss <10%. Causes: High incubator humidity. Very thick shells, as in pullet flocks. Low incubator temperature. Sign: Micromelia (shortened long bones, parrot beak, bent bones); chondrodystrophy (similar to micromelia). Causes: Heredity, lethal genes. Nutritional deficiencies (biotin or manganese). Sign: Short beak, missing beak, face abnormalities. Causes: Incubator temperature too high during days 1 to 5. Heredity, lethal genes. Developmental accidents. Nutritional deficiencies (niacin). Sign: Ectopic (exposed) viscera. Causes: Incubator temperature too high. Heredity, lethal genes. Sign: Hemorrhage. Causes: Red skin -- incubator or hatcher temperature too high. Bleeding in chorioallantois -- rough handling at transfer. Nutritional deficiencies (vitamin K or vitamin E). Embryos that died at days 11 to 15 and appear small and dark red -- usually caused by molds or other contamination. Sign: Swollen head and back of neck (exudative diathesis - increased capillary permeability). Causes: Nutritional deficiencies -- vitamin E or selenium.
Here's some more information on nutritional causes http://www.avianweb.com/deadinshell.html Nutrient Deficiency Signs: Vitamin A Death at about 48 hours of incubation from failure to develop the circulatory system; abnormalities of kidneys, eyes and skeleton Vitamin D Death at about 18 or 19 days of incubation, with malpositions, soft bones, and with a defective upper beak prominent. Please click on this link for info. Vitamin E Early death at about 84 to 96 hours of incubation, with hemorrhaging and circulatory failure (implicated with selenium). Thiamin High embryonic mortality during emergence but no obvious symptoms other than polyneuritis in those that survive. Riboflavin (Vitamin B2) Mortality peaks at 60 hours, 14 days, and 20 days of incubation, with peaks prominent early as deficiency becomes severe. Altered limb and beak development, dwarfism and clubbing of down are defects expressed by embryo. Niacin Embryo readily synthesizes sufficient niacin from tryptophan. Various bone and beak malformations occur when certain antagonists are administered during incubation. Biotin High death rate at 19 days to 21 days of incubation, parrot beak, chondrodystrophy, several skeletal deformities and webbing between the toes. Perosis. Pantothenic acid Deaths appear around 14 days of incubation, although marginal levels may delay problems until emergence. Variable subcutaneous hemorrhaging and edema; wirey down in poults. Pyridoxine Early embryonic mortality based on antivitamin use. 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.
