Cytosine and uracil are converted into beta-alanine and later to malonyl-CoA which is needed for fatty acid synthesis, among other things. Thymine, on the other hand, is converted into β-aminoisobutyric acid which is then used to form methylmalonyl-CoA.  The leftover carbon skeletons such as acetyl-CoA and Succinyl-CoA can then be oxidized by the citric acid cycle. Pyrimidine degradation ultimately ends in the formation of ammonium, water, and carbon dioxide. The ammonium can then enter the urea cycle which occurs in the cytosol and the mitochondria of cells.
Pyrimidine bases can also be salvaged. For example, the uracil base can be combined with ribose-1-phosphate to create uridine monophosphate or UMP. A similar reaction can also be done with thymine and deoxyribose-1-phosphate.
Deficiencies in enzymes involved in pyrimidine catabolism can lead to diseases such as Dihydropyrimidine dehydrogenase deficiency which has negative neurological effects.