Pichia pastoris is a widely used host system for heterologous protein expression both for basic research and industrial production purposes. Recent developments expanding the P. pastoris protein expression toolbox reflect the increasing interest in the application of yeast expression systems for protein-based pharmaceutical products, as an alternative to Escherichia coli and mammalian cell factories. The commonly used expression system for P. pastoris and the recent patents relevant to the P. pastoris genetic toolbox for recombinant protein production are reviewed.