We integrated five sets of proteomic data profiling the constituents of cerebrospinal fluid (CSF) derived from Huntington’s disease (HD) affected and unaffected individuals with genomic data profiling various human and mouse tissues, including the human HD brain. Based on an integrated analysis, we found that brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma, that brain-specific proteins tend to decrease in HD CSF compared to unaffected CSF, and that 81% of brain-specific proteins have quantitative changes concordant with transcriptional changes identified in different regions of HD brain. The proteins found to increase in HD CSF tend to be liver-associated. These protein changes are consistent with neurodegeneration, microgliosis and astrocytosis known to occur in HD. We also discuss concordance between laboratories and find that ratios of individual proteins can vary greatly but the overall trends with respect to brain- or liver specificity were consistent. Concordance is highest between the two laboratories observing the largest numbers of proteins.