To analyse the displacement of surgical clips in prone (Pr) position and assess the consequences on target volumes and integral dose of partial breast irradiation (PBI). 30 post-lumpectomy breast cancer patients underwent CT imaging in supine (Su) and Pr. Clip displacements were measured by the distances from the clips to a common fix bony reference point. On each dataset, the tumour bed (TB = clips ± seroma), clinical target volume (CTV = TB + 1.5 cm) and planning target volumes (PTV = CTV + 1 cm) for PBI were determined and the volume pairs were compared. Furthermore estimation of integral dose ratio (IDR) within the breast from tangential treatment was performed as the ratio of the irradiated breast volume and the volume encompassing all clips. Clips close to the chest wall (CW) in Su showed significantly less displacement in Pr. The mean volumes of seroma, CTV and PTV were significantly higher in Pr than in Su. The PTV volume difference (Pr-Su) was significantly higher in patients with presence of seroma, deep clips and TB location in the superior-internal-quadrant (SIQ) and at the junction of superior quadrants (jSQ). In a multivariate analysis two factors remained significant: seroma and TB localization in SIQ-jSQ. The IDR was significantly larger in Su than in Pr (7.6 vs. 4.1 p < 0.01). Clip displacements varied considerably with respect to their relative position to the CW. In selected patients Pr position potentially leads to a significant increase in target volumes of PBI. Tangential beam arrangement for PBI should be avoided, not only in Su but in Pr as well in case of clip-based target volume definition.