The present study aims to analyse the effect of motivational variables and previous academic achievement on students' future choice of chemistry once this subject becomes optional in the educational system. Toward this goal, the translation and adaptation of the Science Motivation Questionnaire II (SMQII) has been undertaken in our investigation to measure students' motivation towards physics and chemistry. The sample comprised 1060 secondary school Spanish students divided into two groups: 695 students who chose the subject when it became optional for the first time and 365 who decided to leave it. Factor analysis confirmed the original structure of latent variables in our sample, providing validity for this adaptation to a new language and context. A segmentation analysis confirmed that career motivation was the best predictor of students' retention in physics and chemistry before previous academic achievement and the rest of the motivational variables. Although significant gender differences were found in self-efficacy and self-determination, these seem not to be relevant in students' choice.