Single-nucleotide polymorphisms within microRNA (miRNA) binding sites comprise a novel genre of cancer biomarkers. Since miRNA regulation is dependent on sequence complementarity between the mRNA transcript and the miRNA, even single-nucleotide aberrations can have significant effects. Over the past few years, many examples of these functional miRNA binding site SNPs have been identified as cancer biomarkers. While most of the research to date focuses on associations with cancer risk, more and more studies are linking these SNPs to cancer prognosis and response to treatment as well. This review summarizes the state of the field and draws importance to this rapidly expanding area of cancer biomarkers.