Somatic cell count (SCC) is of economic importance in dairy production as it directly influences the revenue from the sale of milk. The current study was carried out to determine the economic value of SCC in South African Holstein and Jersey cattle, in order to establish its relative emphasis in breeding objectives. Bulk-tank SCC was calculated from individual cow test-day SCC for 183 Jersey and 209 Holstein herds that participated in the national milk recording scheme in 2012. SCC premium schemes of the two major milk buyers in the country were used, and herds belonged to either a concentrate-fed or pasture-based production system. The economic value of SCC was determined as the simulated change in profit per cow per year, following a 1% increase in individual bulk-tank SCC. Estimated breeding values (EBVs) are based on log10 transformed SCC (somatic cell score, SCS); therefore the final economic value was expressed in South African rand (ZAR) per SCS. Relative economic values, standardized to the value of protein, were used to compare the relative importance of SCS with other objective traits. An increase in SCS by one unit resulted in decreases in profit ranging from ZAR 491.48 to ZAR 1795.57 per cow per year, depending on the breed, production system and payment system. Economic value was nearly double in the Holstein compared with the Jersey, as well as in the concentrate-fed system relative to the pasture-based system. SCS was among the most important traits in the breeding objective, its value ranging from 26% to 118% compared with the most important trait, protein. High relative emphasis should therefore be placed on SCS in breeding objectives for Holstein and Jersey cattle in South Africa.