Lipid modification of cellular proteins plays diverse roles in the regulation of such proteins' trafficking, signaling and behavior. Owing to a lack of robust detection technologies, the mechanisms by which lipids regulate proteins are poorly understood. Recently, various groups have developed innovative chemical probes in conjunction with bio-orthogonal chemistry for the detection of lipid-modified proteins in vitro and in vivo. These new methods enable further understanding of the mechanisms of protein lipidation and its function in physiology and disease. Here we present a comprehensive summary of these detection probes for monitoring fatty acylation and prenylation, and we provide a perspective on their current and future applications.