The overarching goal of this study is to identify risk factors associated with canine stillbirths, fading puppy syndrome, neonatal losses and perinatal health to make data-driven recommendations for improving puppy survival in guide dog colonies. Perinatal and neonatal deaths account for a significant percentage of all puppies born each year. Our current knowledge regarding intervention and prevention strategies is based solely on past experience and less on data-supported recommendations. This study seeks to quantify the effects of different whelping interventions on puppy outcomes, which will allow informed decision making when handling obstetrical complications with an emphasis on reducing neonatal losses. Furthermore, transfer of bacteria from the vagina of the mother, particularly Group B Streptococcus, to babies during labor has been shown in humans to result in increased risk of neonatal septicemia1. In puppies, bacterial infections represent the second leading cause of mortality and morbidity2. Low-grade bacterial infection of the fetal fluids has also been associated with premature labor in humans. Therefore, monitoring of vaginal bacteria during late pregnancy may be able to predict animals at increased risk of stillbirths and fading puppy syndrome, where antimicrobial treatment may be beneficial. Outcomes of this study will determine if prepartum monitoring is useful and if future studies examining the use of the antimicrobial treatment in high-risk pregnancies is indicated. Preliminary evaluation of one guide dog breeding colony shows about 3% of live puppies born died within the first two weeks of life. Fading puppy syndrome describes the condition where apparently healthy puppies begin to ‘fade’ and most die despite treatment. Bacterial agents most commonly isolated from these cases include Streptococcus, Staphylococcus, and Escherichia coli but other more fastidious bacteria such as mycoplasma and ureaplasma may also be important. Sequencing the bacterial DNA will allow detection of even fastidious bacteria in a relatively cost-effective manner. The vaginal microbiome is also not described in canines, and this study will increase our understanding of how microbes in the vagina interact with the host in health and disease. If the presence of specific bacteria in the vagina is associated is puppy outcomes, treatment options such as antimicrobials or probiotics may be able to reduce puppy losses and diseases.