Introduction: The debate over the education of immigrant pupils relative to native Spanish students is currently a hot topic, but very little research has been undertaken in this area in Spain. The objective of this study was to detect certain possible differences in motivation and strategies between immigrant and Spanish pupils, and also between boys and girls. Method: A sample of 436 secondary school pupils was used. The Motivated Strategies for Learning Questionnaire (MSLQ) was used as a basis, but was adapted in the shape of the elimination of the goal sub-scales (intrinsic and extrinsic), which were replaced by the Goal Orientation Scale of Skaalvik. Various Student's t-tests were carried out to determine whether or not there were statistically significant differences between the independent samples studied, concretely in respect of nationality of origin and of gender. In interpreting results, account was also taken of the effect of the size of sample. Moreover, MANOVA analyses were also used to check whether there were any interactions between the nationality of origin and gender in respect of the variables studied. Results: In general, it was noteworthy that the main differences found were linked to the gender of pupils, much more than their nationality of origin. Hence, statistically significant differences were found in a total of twelve variables by gender and only three by nationality. Moreover, differences encountered lay mostly in the area of learning strategies rather than in academic motivation and self-motivation. Discussion and conclusion: As a general conclusion for this study, it may be emphasized that the main differences recorded were in respect of gender, much more than with regard to the nationality of origin. More specific studies would be desirable so as to develop further this line of investigation, which is novel in a Spanish context.