Association and degradation of protein complexes play essential role in a majority of normal and pathologic processes, which take place in living cell. Studying the underlying mechanisms of those interactions would give deeper understanding of specific causes of disease progression and would allow developing new therapeutic strategies. The majority of technical approaches currently used for detecting protein association include in vitro protein extraction and purification, whereas more relevant results require methods that can be used in vivo. One of a few approaches for in vivo protein association detection is based on reporter protein fragment complementation. Reporter systems based on protein complementation rely on reconstitution of reporter protein fluorescent or enzymatic activity which occurs upon reassociation of protein fragments and could be measured by colorimetry, luminometry or fluorimetry. Protein complementation is widely used to develop reporter systems for analysis of protein interactions, for functional dissection of signal transduction pathways and for performing high-throughput screenings to discover new protein interaction partners. Currently developed approaches that utilize protein fragment complementation have possibilities that extend far beyond simple detection of interaction in a pair of proteins.