The quality of teaching and learning has been one of the major concerns of foundation chemistry disciplines for science and engineering undergraduates at the University of Aveiro, Portugal. Student-centred approaches are being continuously developed, exploring ways of stimulating active and meaningful student learning by encouraging questioning by students. The development of questioning competences is regarded as fundamental, particularly in science education. In order to reinforce adequate alignment with teaching strategies, a new assessment method was implemented during the academic year of 2004-2005. This study is mainly aimed at exploring the use and integration of students' questions as alternative assessment tools. Written formative and summative problem-based cases were designed for these purposes. The questions raised by students during those assignments were analysed according to their cognitive level, relationship and orientation to the problem posed, herein considered to be quality indicators for learners' questions. The findings suggest a deep engagement of students within these situations along the year, supporting the use of these alternative assessment tools as a way of fostering students' questioning capability. Results also reveal that it is possible to achieve, with students' questions placed at the centre of these processes, alignment between teaching, learning and assessment. (Contains 5 tables and 5 figures.)