In order to attain a reliable laboratory work assessment, we argue taking the Learning Environment as a core concept and a research paradigm that considers the factors affecting the laboratory as a particularly complex educational context. With regard to Laboratory Learning Environments (LLEs), a well known approach is the SLEI (Science Laboratory Environment Inventory). The aim of this research is to design and apply an alternative and qualitative assessment tool to characterize Laboratory Learning Environments in an introductory course of organic chemistry. An alternative and qualitative assessment tool would be useful for providing feed-back for experimental learning improvement; serving as a complementary triangulation tool in educational research on LLEs; and generating meaningful categories in order to design quantitative research instruments. Toward this end, spontaneous questions by students have been chosen as a reliable source of information. To process these questions, a methodology based on the Grounded Theory has been developed to provide a framework for characterizing LLEs. This methodology has been applied in two case studies. The conclusions lead us to argue for using more holistic assessment tools in both everyday practice and research. Likewise, a greater attention should be paid to metacognition to achieve suitable self-perception concerning students' previous knowledge and manipulative skills.