The present disclosure provides cytometric methods for the detection of rare target cells in a sample. In certain aspects, the methods and compositions may facilitate the detection of rare target cells, such as circulating tumor cells (CTCs), in a biological sample such as blood. Aspects of the methods include contacting the sample with first and second binding members that specifically bind to a marker of the rare target cell, and cytometrically assaying the sample for the presence of cells comprising bound first and second binding members to detect the rare target cell in the sample. Also provided are systems, compositions, and kits for practicing the subject methods.