Baseball is an international sport with participation from tens of thousands of people worldwide. In the United States, the Prospect Development Pipeline (PDP) is a collaborative effort between Major League Baseball and USA Baseball to establish a developmental pipeline leading to the professional draft. Players participating in the PDP undergo comprehensive evaluations that measure athletic performance, speed-of-processing, visual function, and on-field talent. The present study evaluated data from 1352 elite junior male PDP participants (aged 14 to 21) who signed informed consent, collected between 2017 and 2020, to identify latent abilities and their association with player specialization. Data were first subjected to Exploratory Factor Analysis (EFA) to reduce the 22 measured variables to a smaller set of latent abilities. The resulting factors were evaluated using multiple linear regression to predict each factor using age, height, weight, and position. EFA revealed a combination of physical and psychomotor skills accounting for 52% of the overall variance that grouped into four abilities: grip strength, functional vision, explosiveness, and rapid decision-making. Regression analyses demonstrated that these skills are associated with position assignments, controlling for age, weight, and height, and revealed that outfielders are the most explosive, infielders perform best on psychomotor measures, and catchers perform best on functional vision tests (ps < 0.001). These findings indicate skills that contribute to player specialization, providing new information about the developmental trajectory of junior elite baseball athletes that can be used for scouting and player development.