The paper focuses on the key factors that must be considered when selecting and organising vocabulary suitable for introduction of English through teaching sciences, namely physics and chemistry. The experience draws on participation in a project managed at the Faculty of Education, Masaryk University in Brno, aimed at preparation of vocabulary and methodology materials for teachers of different subjects at Czech lower secondary schools. The teachers, who are not qualified language teachers, collect the relevant vocabulary in the first language, and are to be provided support from the project team, foreign language (English) teachers, whose task is to compile vocabulary books for each subject and prepare the corresponding CLIL methodology. The paper attempts to seek ways to achieving the most logical arrangement and relevant composition of such specialised vocabularies. The collected lexical material ranges from single word expressions to complex and compound sentences, from nominal terms to classroom instructions and explanations with multiple predications. The research has used a representative corpus of 1,000 expressions, applying methods of both quantitative and qualitative analyses. Given the diversity of source teaching materials, which are accreditated individually by each of the involved schools (in correspondence with their own Framework Education Programmes), a common approach must be found to arrangement of the vocabulary in order to stress the core elements of each topic on the syllabuses of the subjects, as well as to unify to a certain extent the special and quite heterogeneous components depending on the needs of individual schools. Another limitation is the CLIL methodology, which must be designed so that it fits the foreign language competences of both specialist teachers and their students. Although the collection of lexical material for the project is still in progress, some partial outcomes are already being tested in the real classroom, bringing thus the necessary feedback.