Bioaffinity materials prepared by entrapping highly selective bioligands in the pores of a sol-gel glass offer unique advantages for the clean-up of complex sample matrices. The inclusion of sol-gel bioaffinity columns frequently allows the efficient elimination of interfering matrix components and enrichment of analytes in a simple step. After introducing the basic principles the paper reviews the methods for the production of protein-doped sol-gel materials and discusses the characteristics of sol-gel affinity columns by comparing their stability, selectivity, binding capacity and reusability. The potential of sample clean-up with sol-gel affinity columns is demonstrated giving applications in environmental, food and clinical analysis.