In recent years, several methods have been developed to analyze protein-protein interactions under native conditions. One of them, tandem affinity purification (TAP), combines two affinity-purification steps to allow isolation of high-purity protein complexes. This unit presents a methodological workflow based on an SF-TAP tag comprising a doublet Strep-tag II and a FLAG moiety optimized for rapid as well as efficient tandem affinity purification of native proteins and protein complexes in higher eukaryotic cells. Depending on the stringency of purification conditions, SF-TAP allows both the isolation of a single tagged-fusion protein of interest and purification of protein complexes under native conditions.