Multiple tools for the molecular analysis of variation at both the DNA and protein level have recently been developed. These molecular tools that include low cost sequencing, simultaneous genotyping of large numbers of single nucleotide polymorphisms chips, real-time polymerase chain reaction (PCR) and RNAseq (for gene expression) are enabling scientists to better understand the fundamental bases of egg-quality traits in poultry. Genomic selection methods have been developed to improve egg quality and have been implemented by major poultry breeding companies. This chapter looks at ways to improve external egg quality and internal egg quality utilizing these molecular tools. The Animal Genome Quantitative Trait Loci (QTL) database currently includes 4676 chicken QTLs curated from 224 publications for 316 different chicken traits (www.animalgenome.org). Targeted genomic analysis of specific genes allows in-depth study of genes involved in the determination of egg quality. Further insights are gained with gene expression and regulation studies.