This study was conducted to determine the potential of lactoperoxidase (LP) for the diagnosis of subclinical mastitis in goats. The activities of LP and somatic cell counts (SCC) were determined in the milk of clinically healthy Saanen and South African Indigenous goats and the correlation between LP activity and SCC was measured. An increase in LP activity was observed with increasing number of somatic cells in the milk of the two goat breeds. A significantly (p < 0.01) positive correlation was observed between LP activity and SCC in the Indigenous (r = 0.91) and Saanen (r = 0.95) goat milk samples. The mean SCCs in Indigenous and Saanen goat milk samples were 2.5 × 104 and 2.0 × 106 cells/ml, respectively. The LP activity of Saanen goat milk ranged from 0.49 to 1.07 units/ml with a mean value of 0.80 units/ml. In the Indigenous goat milk, the LP activity ranged from 0.03 to 0.38 units/ml with a mean value of 0.26 units/ml. The positive correlation observed between SCC and LP activity suggests that LP may be used to detect subclinical mastitis in dairy goats.