The aim of the present study was to compare the recolonization pattern of mutans streptococci on densely colonized teeth with and without fixed orthodontic appliances after treatment with a 40 per cent chlorhexidine (CHX) varnish (EC 40, Explore). Healthy subjects free of carious lesions requiring fixed orthodontic appliance treatment but with high bacterial mutans streptococci saliva counts were recruited (n = 10). For baseline registration, plaque from buccal sites was sampled and cultivated on Dentocult strips. Following professional tooth cleaning, CHX varnish was applied to all teeth for 8 minutes. Subsequently, orthodontic brackets and bands were inserted in either the upper or lower arch. Eight weeks after varnish application the degree of recolonization with mutans streptococci was reassessed on the buccal sites. Statistical analysis showed that recolonization with mutans streptococci was significantly higher (P < 0.05) on teeth with orthodontic appliances. The results indicate that the use of fixed orthodontic appliances creates artificial environments suitable for the proliferation of mutans streptococci after CHX varnish suppression.