This study investigated the ability and efficacy of an Er:YAG laser with a fluorescence feedback system for caries removal in deciduous teeth. Seventy-nine carious lesions were excavated using a fluorescence-controlled Er:YAG laser. Endpoint of treatment was defined by emission of fluorescence from the dentine surface below the pre-selected threshold level of 7 units and the subsequent termination of Er:YAG laser radiation. Dentine samples were obtained from the cavity floor, and viable counts of both Streptococcus mutans and Lactobacilli, expressed as colony forming units (log CFU), were evaluated. Preparation time was recorded to assess efficacy of the treatment procedure. S. mutans and/or Lactobacilli were found in 25 out of 79 lesions. Regarding the counts for S. mutans and Lactobacilli, the median log CFU was 0 (min, 0; max, 5.5) and 0 (min, 0; max, 6), respectively, with 2.4% of all samples yielding more than 100 CFU S. mutans and 4.8% yielding more than 100 CFU Lactobacilli. In 8 out of 79 cases, laser excavated cavities were not judged being caries-free using the conventional tactile criterion for assessing caries tissue. Focussing on these teeth, the median log CFU was 0 (min, 0; max, 0.5) for S. mutans and 0 (min, 0; max, 1.6) for Lactobacilli. The mean time for treatment was 2.3+/-1.2 min. Of the children, 93.8% rated the laser treatment to be comfortable. The study indicates that the fluorescence feedback-controlled Er:YAG laser might be an appropriate device for caries removal in children using the suggested threshold level of 7 units.