Program Visualization (PV) is believed to be useful in Computer Science education. However, while some PVs have been found to help users learn, other PVs have not been beneficial. In this thesis we studied the users gaze pattern to find effects of popup questions on an individuals visual attention. We further analyzed the correlation of gaze behavior with the individuals preferred learning style, performance based on a pre-test and post-test and a variety of perceptual, attentional and cognitive abilities as determined by a battery of paper-and-pencil and computer-based assessments. While popups appear to be effective for directing attention, no significant effect on comprehension of the depicted algorithm was detected. Individual with different learning styles have distinctive viewing patterns and this finding should be utilized in designing PVs that consider individual differences.