The aim of the research was to examine pupils' preferences of learning modalities and approaches to learning Mathematics and Science. Furthermore, it was examined whether the approach to learning was related to the pupils' perception of their interest for the subjects and grades from the mentioned subjects and whether they differ depending on whether they like to learn or not. The survey was conducted on a sample of 63 third and fourth grade pupils in one elementary school. Of the total sample, there were 30 girls (47.6%) and 33 boys (52.4%). The age range of pupils is between 9 and 11 years. The results of the research have generally shown that there is no difference in school success in Mathematics and Science between pupils who like and dislike learning, and pupils who like to learn perceive both subjects more interesting. When it comes to pupils' preferences of learning modality, most of them are in the auditory category and slightly less in the kinesthetic and visual categories. Furthermore, pupils estimate that they are more prone to deep than surface approach while learning Mathematics and Science. Deep approach to learning is positively correlated with the interest for the subject, and surface approach is negatively correlated with the interest for the subject. Pupils who are more inclined to the surface approach to learning Mathematics also have poorer grades in Mathematics, while in other cases there is no correlation between grades and approaches to learning. Finally, pupils who are more prone to deep approach to learning generally express greater preference of visual, auditory and kinesthetic learning modalities.