We evaluated the inter-physician variability in the target contouring of the radiotherapy for anal squamous cell carcinoma (ASCC). Clinical target volume (CTV) of three patients diagnosed with ASCC was delineated by seven experienced radiation oncologists from multi-institution. These patients were staged as pT1N1a, cT2N0, and cT4N1a, respectively, according to 8th edition of the American Joint Committee on Cancer staging system. Expert agreement was quantified using an expectation maximization algorithm for Simultaneous Truth and Performance Level Estimation (STAPLE). The maximum distance from the boundaries of the STAPLE generated volume with confidence level of 80% to those of the contour of each CTV in 6 directions was compared. CTV of pelvis which includes primary tumor, perirectal tissue and internal/external iliac lymph node (LN) area (CTV-pelvis) and CTV of inguinal area (CTV-inguinal) were obtained from the seven radiation oncologists. One radiation oncologist did not contain inguinal LN area in the treatment target volume of patient 2 (cT2N0 stage). CTV-inguinal displayed moderate agreement for each patient (overall kappa 0.58, 0.54 and 0.6, respectively), whereas CTV-pelvis showed substantial agreement (overall kappa 0.66, 0.68 and 0.64, respectively). Largest variation among each contour was shown in the inferior margin of the CTV-inguinal. For CTV-pelvis, anterior and superior margin showed the biggest variation. Overall, moderate to substantial agreement was shown for CTV delineation. However, large variations in the anterior and cranial boarder of the CTV-pelvis and the caudal margin of the CTV-inguinal suggest that further studies are needed to establish a clearer target volume delineation guideline.