The parasites that cause severe malaria appear to increase expression of a restricted, but poorly defined, subset of the PfEMP1 variant, surface antigens. PfEMP1s are major targets of protective immunity. Here we used RNASeq to analyse gene expression in 44 parasite isolates that caused severe and uncomplicated malaria in Papuan patients. We identified novel associations between disease severity and PfEMP1 transcripts, domains and smaller sequence segments as well as confirming all previously reported associations between expressed PfEMP1 sequences and severe disease. These findings will inform efforts to identify vaccine targets for severe malaria.