Autism Spectrum Disorder is a class of developmental disabilities characterized by social, communication, and behavioral impairments that has a wide range of severity between individuals. Studies have shown these defects stem from abnormal brain development during crucial developmental stages during early development. The underlying genetic cause of these impairments is not well understood but is believed to be a combination of a complex pairing of genetic and environmental factors. Several papers have indicated that topoisomerase 3B (top3b) plays a role in phenotypic defects in mice and fruit flies role indicating a defect in synaptic formation, a key component in developing verbal and social skills. These hindered neural circuits could potentially be the cause of the cognitive deficits characteristic in Autism. Our current research aims to better understand the specific roles of top3b in early neurological development though an in vivo study using zebrafish embryos as a vertebrate model system. We used a technique called RNA in situ hybridization and identified the regions of zebrafish nervous system where top3b is present during early neural development. We identified top3b is present in the forebrain, notochord, and visual neural pathways. Further, we used anti-sense nucleotides and created top3b deficiency in zebrafish embryos. Top3b deficient zebrafish embryos revealed defects in spinal motor nerves in the trunk and visual neural pathways in the head. We labeled the motor nerves and their muscle targets (Acetylcholine receptors) using molecular labeling techniques and identified that top3b deficient embryos lack connectivity of nerves and their target muscles. Further, when we re-introduce top3b RNA into deficient embryos, the defects were largely reduced and the embryos develop with normal spinal and visual neural pathways and are able to make connections to their muscle targets. Activation of Acetylcholine receptors have been shown to produce a variety of behavioral and physiological effects such as cognitive performance, vigilance, locomotor activity, respiration, and cortical blood flow. Location of top3b regions and the defect patterns seen in the deficient embryos implicate top3b plays a role in visual neural pathways and neuromuscular connectivity. Developing and analyzing the top3b deficient zebrafish model would enable us to use this model to identify potential drug targets against human neurological disorders such as autism.