Quality control (QC) is a fundamental area of management for semen production centers (SPCs) supplying bovine semen to breeders and producers. Semen production centers are moving away from subjective semen assessment, that is largely uncorrelated to field fertility, to objective semen analyses that incorporate computer assisted sperm analysis (CASA) and flow cytometry. A multiparametric approach to semen analysis using a combination of CASA and flow cytometry can provide SPCs with the highest QC for all semen production. In this paper we review probes used for labelling spermatozoa for viability, acrosomal integrity, mitochondrial activity, DNA integrity and calcium release. Limitations of CASA and flow cytometry when analyzing spermatozoa, especially frozen-thawed samples, are discussed. Finally, we described how a multiparametric approach using CASA and flow cytometry could be applied in SPCs to establish QC of production before the release of the product in the field