Fluorescence Correlation Spectroscopy (FCS) has developed into a routine method to quantitatively study diffusion of molecules and kinetic processes. FCS has recently become popular to complement live cell imaging with biophysical information. The enabling technology has been commercially realised by combining laser scanning microscopes and fluorescence correlation spectrometers in one integrated platform. This article provides an overview of the Zeiss solution of such a combined instrument, the LSM 510 META / ConfoCor 2 system. We focus on the instrumental set up as well as technical advances and improvements in the software that controls FCS data acquisition and evaluation. In addition, we outline the calibration of the instrument and the work flow for data analysis with emphasis on in vivo pharmacological applications.