Owing to their outstanding inherent thermal stability and proteolytic resistance, as well as their small size of only around 30 amino acid residues, cystine knot miniproteins are an attractive class of agents for the development of peptide-based pharmaceuticals. Many natural miniproteins already possess interesting pharmacological properties that can be used as starting point for further improvement by protein engineering. Cystine knot miniproteins, also known as knottins, are readily accessible by recombinant bacterial production or by solid phase chemical synthesis. Potent and selective knottins with predefined binding characteristics were obtained by rational protein design as well as by combinatorial library screening. Owing to their proteolytic stability and relatively high rates of intestinal uptake, the oral administration of miniproteins seems to be within reach. With the first engineered knottin successfully applied for tumor imaging and several others being already marketed as analgesic or in preclinical and clinical development, it can be expected that more tailor-made diagnostic and therapeutic cystine knot miniproteins will follow over the next years.