In this study, the effect of 3 cognitive variables such as logical thinking, field dependence/field independence, and convergent/divergent thinking on some specific students' answers related to the particulate nature of matter was investigated by means of probabilistic models. Besides recording and tabulating the students' responses, a combination of binomial and multinomial logistic regression techniques was used to analyze the data. Thus, students' misconceptions as well as the compatible-with-the-scientific-view student's answers were explored one by one in relation to the above 3 cognitive variables. The study took place with the participation of 329 ninth-grade junior high school pupils (aged 14-15). The results showed that mostly logical thinking and sporadically the other 2 cognitive variables were significantly associated with students' answers. Interpretation of the results and implications for science education are discussed.