Fixed orthodontic treatment has been shown to cause an increased incidence of enamel demineralisation. The purpose of this study was to investigate the changes in stimulated salivary flow rate, pH, buffer capacity, and the levels of mutans streptococci (MS) and lactobacilli in patients undergoing therapy with fixed orthodontic appliances. Saliva samples, plaque index scores and dietary histories were taken from 21 sequential patients before the start of treatment, and one month and three months after placement of brackets and bands. There was a statistically significant increase in stimulated salivary flow rate, pH, buffer capacity, plaque index scores, and in the levels of MS and lactobacilli after three months of active treatment. It is postulated that the balance between the cariogenic challenge posed by high levels of MS and lactobacilli, and the reparative effects of concurrent increases in salivary flow rate, pH and buffer capacity, determines the likelihood of mineral loss or gain over time. A failure to follow basic preventive measures may increase the risk for some patients of enamel decalcification during orthodontic treatment with fixed appliances.