A high throughput Microtiter plate Cell Retainer (MCR) has been developed to enable, for the first time, high-content, time-dependent analysis of the same single non-adherent and non-anchored cells in a large cell population, while bio-manipulating the cells. The identity of each cell in the investigated population is secured, even during bio-manipulation, by cell retention in a specially designed concave microlens, acting as a picoliter well (PW). The MCR technique combines micro-optical features and microtiter plate methodology. The array of PWs serves as the bottom of a microtiter plate, fitted with a unique flow damper element. The latter enables rapid fluid exchange without dislodging the cells from their original PWs, thus maintaining the cells' identity. Loading cell suspensions and reagents into the MCR is performed by simple pouring, followed by gravitational sedimentation and settling of cells into the PWs. Cell viability and cell division within the MCR were shown to be similar to those obtained under similar conditions in a standard microtiter plate. The efficiency of single cell occupancy in the MCR exceeded 90%. No cell dislodging was observed when comparing images before and after bio-manipulations (rinsing, staining, etc.). The MCR permits the performance of kinetic measurements on an individual cell basis. Data acquisition is governed by software, controlling microscope performance, stage position and image acquisition and analysis. The PW's unique micro-optical features enable rapid, simultaneous signal analysis of each individual cell, bypassing lengthy image analysis.