Massively parallel sequencing (MPS) has facilitated a significant increase in transcriptomic studies in all biological disciplines. However, the analysis of degraded RNA remains a genuine challenge in practice. In forensic science the biological samples encountered are often extensively degraded and of low abundance. RNA from these compromised samples is used for body fluid identification through the detection of body fluid-specific transcripts. Here we demonstrate the sequencing of four forensically relevant body fluids: oral mucosa/saliva (buccal), circulatory blood, menstrual blood and vaginal fluid. RNA was extracted from fresh, two and six week aged samples. Despite the extensive degradation of most body fluids, significant high quality sequencing output (>80% sequence above Q30) was generated. An average of over 80% of reads from all but one sample aligned successfully to the reference human genome. Furthermore, FPKMs (fragments per kilobase of exon per million fragments mapped) generated indicate the accurate detection of known body fluid markers in respective body fluids. Assessment of global gene expression levels over degradation time enabled the characterisation of differential RNA degradation in different body fluids. This study demonstrates the practical application of MPS technology for the accurate analysis of degraded RNA from minimal samples.