Reproductive failure is ubiquitous. However, research on the mechanisms underpinning reproductive failure is still lacking in most species. This gap in our understanding has particularly strong repercussions for threatened species and it hinders our ability to establish effective interventions to improve survival. In this review, we focus on why eggs fail to hatchone of the most critical and understudied aspects of bird reproduction. We identify the main drivers of hatching failure in threatened populations of birds and the key mechanisms that cause failure at different stages of development inside the egg. We then discuss the importance of management interventions aimed at reducing hatching failure in species of conservation concern. Our review highlights the need for a better understanding of the mechanistic basis of hatching failure in non-model bird species and identifies the methodological tools necessary to achieve this.

1. Early embryo mortality has recently been proven to be a significant component of avian reproductive failure. Due to the difficulty in distinguishing eggs which have suffered early embryo mortality from unfertilised eggs, this cause of reproductive failure has historically been underestimated and overlooked. 2. We describe methods for recognising and collecting undeveloped, unhatched eggs from wild bird populations, identifying and isolating embryonic material in unhatched eggs, and efficiently extracting DNA from those samples. We test these methods on unhatched eggs collected from the field which have undergone post-mortem incubation. 3. We obtained DNA yields from early-stage embryos that are sufficient for a wide range of molecular techniques, including microsatellite genotyping for parentage analysis and sex-typing. The type of tissue sample taken from the egg affected downstream DNA yields and microsatellite amplification rates. Species-specific microsatellite markers had higher amplification success rates than cross-species markers. We make key recommendations for each stage of the sampling and extraction process and suggest potential protocol improvements and modifications. 4. Genetic and possibly genomic analysis of embryos that die early in development has the potential to advance many fields. The methods described here will allow a more in-depth exploration of the previously overlooked causes of early embryo mortality in wild populations of birds, including threatened species.