This paper reports on the autonomy Grade 9 learners (13-14 years) are given when doing science investigations. The study adopted a mixed methodology research design which involved the collection of both quantitative and qualitative data. Quantitative data were collected by means of questionnaires which were administered to 55 teachers. Qualitative data were collected by means of teacher interviews. The general trends that were quantitatively established were validated and explicated by the qualitative analysis. A finding of the study was that at schools where science investigations are taking place, learners have varying degrees of autonomy across the different stages of the investigation. In general, autonomy increases from little autonomy at the initial stage when formulating the investigation question to significant autonomy in drawing conclusions. In terms of the classification framework described in the paper, investigations which are taking place are largely structured investigations where the teacher exercises a great deal of control over the stages of the investigation. The findings also explain why teachers choose structured investigations for their learners.