We report on an innovative approach to on-chip detection of single fluorescently-labeled magnetic micro-particles by means of Single Photon Avalanche Diode (SPAD) arrays. Our system enables particle separation through magnetic actuation and highly sensitive, high signal-to-noise-ratio detection with integrated SPADs. We will present the capability of our system to detect and quantitatively distinguish fluorescently labeled particles. This represents a first step towards a complete lab-on-a-chip system for specific antibody detection. The selection of magnetic micro-particles as the mobile substrate in a bio-assay is motivated by their growing impact on the lab-on-a-chip research area, fueled by their ability of contactless manipulation and a handling that is independent from biological processes.