This dissertation examines the cognitive processes individuals use when reading organic chemistry equations and factors that affect these processes, namely, visual complexity of chemical equations and participant characteristics (expertise, spatial ability, and working memory capacity). A six stage process model for the comprehension of organic chemistry notation was proposed that accounts for the movement of the eyes across the chemical equation (get next); the search of a chemical structure for key features (search); the encoding of features to create an internal representation (encoding and access lexicon); the assignments of relationships among features in the same molecule (intramolecular relationship) and between molecules (intermolecular relationship); and a check of the internal representation for inconsistencies (reaction wrap-up). Two studies were conducted in this investigation. The first study assessed the validity and ability of the "Complexity Rubric for Organic Chemistry Notation" to quantify visual complexity of structural formulas. A three-part investigation examined the content of the rubric, its capacity to measure visual complexity, and its ability to predict visual complexity as perceived by novices. The results suggest that the rubric differentiates structural formulas with high visual complexity from those with medium-low visual complexity. A follow-up study examined the effect of prior knowledge on the encoding of organic formulas and suggests that knowledge from domains outside chemistry plays a role in the perceived complexity of structural formulas. In the second study, eye tracking methodology was used to validate the proposed process model for the comprehension of organic chemistry notation and examine factors that affect these processes. Eight instructors and 19 students were eye tracked while reading five high/low complexity pairs of organic chemistry equations for comprehension. The frequency, duration, and sequence of participants' eye fixations were examined. The results provide evidence for each stage of the proposed process model and suggest that visual complexity of the equation, as measured by the rubric, significantly affects the viewing patterns of participants. Expertise of the participant was also shown to play a significant role in viewing patterns. The effects of working memory capacity and spatial ability were shown to be less consistent and may be topic dependent. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]