Identifying live eggs includes: a) illuminating eggs with light; b) receiving light passing through each egg at a light detector; c) generating an output signal that corresponds to light received at a light detector for each respective egg; d) analyzing the output signals to identify an indication of an external disturbance; e) analyzing the output signal for each egg to identify the existence of an embryo heart rate and/or embryo movement; and f) designating an egg as a live egg in response to identifying embryo heart rate and/or embryo movement. Steps a) through d) are repeated if output signals from a predetermined number of eggs contain an indication of an external disturbance to the eggs. Steps a) through f) are repeated if the number of eggs designated as live exceeds an expected number, or if embryo movement occurs at about the same time in a predetermined number of eggs.