Insertional mutagenesis by viral vectors is a problem in gene therapy. We recently reported that lentiviral vectors with an intact HIV long terminal repeat (LTR) caused insertional gene activation by transcripts from the 5′ LTR splicing to an adjacent gene. Here we demonstrate that the level of transcription from the 5′ LTR, and also insertional gene activation, is dependent on the internal promoter in the vector. We also show that there are more transcripts originating from the 5′ LTR than from, or reading through, the 3′ LTR. This study will allow the design of safer lentiviral vectors for applications in which an intact HIV LTR is required.