Volatile organic chemicals emitted by a shell egg embryo are used to identify the fertility, viability, and sex of the shell egg embryo. Shortly after the egg is laid, the egg is isolated in a vapor-tight compartment so that a vapor containing volatile organic chemicals emitted by the shell egg embryo collect in the headspace of the compartment. The chemicals in the vapor are analyzed to construct a chemical profile of the shell egg embryo, and then the chemical profile of the shell egg embryo vapor is loaded into a previously developed model. Based on the data generated by the model, the shell egg is embryo is predicted to be an alive male, an alive female, an infertile egg, or an egg containing a dead embryo.