Background: Small intestine neuroendocrine tumors (SI-NETs), also called “carcinoids,” are insidious tumors that are often metastatic when diagnosed. Limited studies on the mutational landscape of small bowel carcinoids indicate that these tumors have a relatively low mutational burden. The development of targeted therapies will depend upon the identification of mutations that drive the pathogenesis and metastasis of SI-NETs. Methods: Whole exome and RNA sequencing of 5 matched sets of constitutional tissue, primary SI-NETs, and liver metastases were investigated. Germline and somatic variants included: single nucleotide variants (SNVs), insertions/deletions (indels), structural variants, and copy number alterations (CNAs). The functional impact of mutations was predicted using Ensembl Variant Effect Predictor. Results: Large-scale CNAs were observed including the loss of chromosome 18 in all 5 metastases and 3/5 primary tumors. Certain somatic SNVs were metastasis-specific; including mutations in ATRX, CDKN1B, MXRA5 (leading to the activation of a cryptic splice site and loss of mRNA), SMARCA2, and the loss of UBE4B. Additional mutations in ATRX, and splice site loss of PYGL, led to intron retention observed in primary and metastatic tumors. Conclusions: We observed novel mutations in primary/metastatic SI-NET pairs, some of which have been observed in other types of neuroendocrine tumors. We confirmed previously observed phenomena such as loss of chromosome 18 and CDKN1B. Transcriptome sequencing added relevant information that would not have been appreciated with DNA sequencing alone. The detection of several splicing mutations on the DNA level and their consequences at the RNA level suggests that RNA splicing aberrations may be an important mechanism underlying SI-NETs.