This study aimed to investigate whether interdental brush shape influences cleaning efficacy, by comparing a waist-shaped interdental brush (W-IDB) with a cylindrical IDB (C-IDB); both provided with the same bristle texture. Cleaning efficacy of differently shaped IDBs was measured in proximal surfaces of teeth in a split-mouth cross-over design. Twenty-eight patients abolished oral hygiene for 4 d. Line angle plaque area was scanned with an intraoral camera after use of disclosing dye in baseline and after IDB application and analyzed planimetrically. Additionally, bacterial load in the IDBs was analyzed after usage by colony forming units (cfu). A Wilcoxon signed-rank test with continuity correction was used to compare the results of the waist-shaped and the cylindrically-shaped IDBs. The waist-shaped IDBs cleaned significantly better than their cylindrically-shaped counterparts (area cleaned: 23.1% vs. 18.3%), when applied at same interdental spaces (p < 0.001). However, no significant differences were found in comparison of bacterial load on the IDBs (median cfu counts: 2.3E9 vs. 2.7E9, p = 0.93). Irrespective of bristle texture or size, IDB shape have impact on cleaning efficacy. Waist-shaped IDBs are more effective in cleaning of the line angle area than cylindrically-shaped IDBs.