Infertility affects 15% of all couples and presents a major public health issue. Animal and human data indicate that epigenetic dysregulation in sperm is associated with poor male reproductive health and extensive epigenetic reprogramming during spermatogenesis presents a window of vulnerability for environmentally-induced epigenetic dysregulation. Phthalates is a class of ubiquitous environmental contaminant and global health concern. Phthalate exposure in humans has been associated with diminished male fertility, adverse birth outcomes, and altered offspring development. In order to facilitate additional research on this topic, we aimed to developing a higher throughput method of sperm nucleic acid extraction. In addition, this dissertation also examined the associations of paternal phthalate exposure with sperm methylation patterns and blastocyst development. In order to maximize efficiency of the limited and difficult to acquire samples while increasing throughput for epidemiologic studies, we developed a novel method of sperm nucleic acid extraction that improved ease and efficiency. Compared to previously published methods, our new method has 1) increased yield of DNA per sperm cell, 2) reduced time required for DNA processing, and 3) eliminated the need for odorous sulfur-based reducing compounds. As part of the Sperm Environmental Epigenetics and Development Study (SEEDS), we recruited 50 couples from an in vitro fertilization (IVF) clinic. We observed that concentrations of select paternal urinary metabolites of phthalates or phthalate alternatives were associated with a marked decrease in blastocyst quality. With respect to sperm DNA methylation, we found that the male urinary anti-androgenic phthalate metabolite concentrations were associated with 131 differentially methylated regions in sperm DNA. Gene ontology analyses revealed that these differentially methylated regions were enriched in genes related to growth and development as well as cellular function and maintenance. Overall, the evidence presented by this dissertation show that paternal adult exposure to select phthalates and phthalate alternatives may influence both embryo development and sperm DNA methylation patterns. Additional work is required to replicate our findings as well as determine whether the observed aberrant sperm DNA methylation patterns associated with urinary metabolites of phthalates and phthalate alternatives are true biological mediators of the concurrent decrease in embryo quality.