I present a novel single photon spectrometer and discuss its use for ultra-fast and highly accurate detection of quantum dots and micro-beads encoded with compositions of various types of quantum dots. The spectrometer receives a polychromatic light through a fiber input. The received light undergoes color decomposition by a diffraction grating and is further detected by a 32-channel PMT (Hamamatsu, Japan) operating in single photon counting mode. Due to a novel, highly advanced analog/digital circuitry operating in GHz range, the 32-channel single photon detector has a unique performance: it supports detection of up to 108 photon/s/channel, data acquisition rate at up to 106 frames/s, data transfer and via Ethernet, and data recording speed up to 32MB/s using a standard PC. Due to an extremely broad linearity range and high data acquisition speed, the developed spectrometer has been successfully used for the detection of fluorescent radiation from both single quantum dots and micro-beads with embedded quantum dots of different colors. Our experiments demonstrated the ability of the spectrometer to detect up to 10,000 micro-particles per second. For the beads with embedded quantum dots of 6 different colors we were able to distinguish up to 105 different color combinations (QDs fluoresce in spectral range between 490nm and 700nm). Currently, in the field of molecular biology there is a wide variety of techniques and assays based on color labeled micro- and nano-particles. The unique detection performance of our single photon spectrometer suggests its successful use in multiple applications such as life sciences, molecular diagnostics, personalized medicine and others.