Content and language integrated learning (CLIL) is burgeoning all over Europe and this is particularly so in Spain. During the last 10 years, content language instruction through a foreign language (FL) (mainly English) has become a key area of curricular innovation. One of the main reasons put forward by the advocates of this approach is that students are more motivated as a result of participating in CLIL programmes. Since motivation is one of the most influential individual variables when it comes to learning an L2, the benefits of the CLIL approach are assumed. However, there is a dearth of studies which empirically confirm differences in motivation when comparing traditional English as a foreign language (EFL) instruction and CLIL. This article aims to shed light on this issue through a study carried out in the Basque Country (Spain) in two different grades. Three hundred and ninety-three compulsory secondary education students (aged 12-13 and 14-15) enrolled in EFL and CLIL courses participated in the study. The data were gathered by means of a previously piloted and validated quantitative questionnaire. The statistical analyses showed that CLIL students were more motivated; however, these results should be analysed with caution, taking into account a series of individual (age and sex) and contextual (socio-cultural) variables that may influence such results. The effect of these variables, which have little to do with the CLIL approach per se, has not always been sufficiently considered when explaining the positive outcomes of CLIL.