Monascus species are used for production of red bio-pigments, which are used as food coloring agents. However, presence of the mycotoxin citrinin, which is a secondary metabolite produced in conjunction with the red pigments, prevents the use of these pigments in large scale. In the present study, Monascus ruber Van Tieghem was isolated from the Egyptian soil and identified. Effect of media composition on nine of the pigments produced by this fungus in addition to citrinin was studied. The fungus was grown in four different media containing different carbon sources (glucose, ethanol, yeast malt extract and potato dextrose broth). On the other hand, effect of glucose concentration was also studied. The produced pigments and citrinin were extracted by butnol and analyzed by LC/MS/MS as well as HPLC with fluorescence detection of citrinin. The data revealed that the highest amount of red pigments production (4.3g/l) was obtained at glucose concentration 10g/l. This was combined with complete absence of citrinin. Rubropunctamine (26.1%) and ankuflavine (48.7%) were the most abundant pigments in the glucose and ethanol media, respectively; while Moanascin (61.6%) and N-glutarylrubropunctamine (39.4%) were the most abundant in the PDB and YMB media, respectively. This result enables the large scale production of the red pigments by M. ruber without production of the mycotoxin citrinin.