The purpose of the present study was to compare in untreated patients suffering from moderate to severe periodontitis the efficacy of dental floss (DF) and interdental brushes (IDB) in the reduction of plaque, gingival inflammation, and probing depth in a 6-week period prior to subgingival debridement. Twenty-six patients (12 female, 14 male; mean age 37.4 years; range 27 to 72 years) were instructed to use DF for one side of the dentition and IDB for the other side as an adjunct to the daily toothbrushing for 6 weeks. Oral hygiene instructions for toothbrushing and the use of the two devices were given at baseline and at week 3. Measurements were carried out at baseline and at 6 weeks including plaque scores, probing depth, and 2 bleeding scores (periodontal pocket bleeding index and angulated bleeding index). With the IDB, the approximal plaque score at baseline of 3.09 reduced to 2.15 at 6 weeks and with DF from 3.10 to 2.47, respectively. IDB proved to remove significantly more plaque than DF. Baseline probing depth of 5.84 mm for IDB sites and 5.59 mm for DF sites was reduced to 5.01 mm at 6 weeks for both regimens. Analysis showed that the use of IDB resulted in a greater pocket reduction. Both bleeding indices were slightly reduced with IDB and DF, but no differences between devices were found. In relation to patient acceptance, more problems were observed with DF, and IDB were felt to be more efficacious. In conclusion, the results of the present study indicate that in combination with a manual toothbrush, the use of interdental brushes is more effective in removal of plaque and results in a larger reduction of probing depth than the use of dental floss. Although the differences were small, they indicate, in combination with patient preferences, that interdental brushes are to be considered preferable to floss for interdental plaque removal in patients suffering from moderate to severe periodontitis.