Compartmentation via filamentation has recently emerged as a novel mechanism for the regulation of metabolism. In order to identify filament-forming metabolic enzymes systematically, we performed a genome-wide screening of all strains available from an open reading frame-GFP collection in Saccharomyces cerevisiae. We discovered 9 novel filament-forming proteins and also confirmed those identified previously. Out of the 4,159 strains, we found 23 proteins, mostly metabolic enzymes, that are capable of forming filaments in vivo. In silico protein-protein interaction analysis suggests that these filament-forming proteins can be clustered into several groups, including translational initiation machinery, glucose and nitrogen metabolic pathways. Using glutamine-utilising enzymes as examples, we found that the culture conditions affect the occurrence and length of the metabolic filaments. Furthermore, we found that two CTP synthases (Ura7p and Ura8p) and two asparagine synthetases (Asn1p and Asn2p) form filaments both in the cytoplasm and in the nucleus. Live imaging analyses suggest that metabolic filaments undergo sub-diffusion. Taken together, our results identify novel filament-forming proteins in Saccharomyces cerevisiae and suggest that filamentation of metabolic enzymes is more general than currently appreciated.