Interest in extracellular vesicle (EV) biology has burgeoned over the past decade since the realisation that these nanomembranous vesicles play seminal roles in the intercellular communication and cell signalling pathophysiology by transferring selected cargo between cells, such as protein, lipid, DNA and RNA. Previously we reported that human LIM1863 colorectal cancer (CRC) cells secret three distinct extracellular vesicle subtypes, shed microvesicles (sMVs) and two exosome populations (immunoaffinity isolated A33-exosomes and EpCAM-exosomes), with distinct protein signatures. We extend our omics approach to understand the RNA profiles including microRNA, mRNA and lncRNA in these EVs. Using small RNA sequencing we identified a total of 254 miRNAs, of them 63 were selectively distributed into these EVs. Six miRNAs (let-7a-3p*, let-7f-1-3p*, miR-451a, miR-574-5p*, miR-4454 and miR-7641) are common enriched to all EV subtypes. Notably, A33-Exos contained the largest number (32) of exclusively-enriched miRNAs; 14 of them have not been reported in the context of CRC tissue/bio-fluid analyses and warrant further examination as potential diagnositic markers of CRC. Next, we used transcriptome sequencing to profile mRNAs and lncRNAs in these three EV subtypes and obtained 2389 mRNAs, 317 pseudogene transcripts, 1028 lncRNAs and 206 short noncoding RNAs selectively distributed into LIM1863 EVs. Further analysis showed 1937 mRNAs encode canonical proteins, 348 isoforms (including splice-variant proteins) and 119 “missing” proteins (without evidence on protein level). Interestingly, we found 151 RNA binding proteins from our proteomics data and 6 of them may have the potential of sorting RNAs into EVs because they can interact with ~75% of the EV-enriched RNAs. Our data also revealed the co-existence of U1 and U2 ribonucleoproteins and their cognate snRNAs in LIM1863 EVs. EV-enriched mRNAs and lncRNAs were validated using paired tumour/normal tissues from 22 CRC patients and the results strengthened their potential of being biomarkers for CRC, in addition, we identified 268 novel splicing events and 33 fusion genes, which can be the resource of neoantigens. Our study will advance our understanding of EV biology in CRC and accelerate the development of EV-based diagnostics and therapeutics.