Side-by-side operations are often used in the offshore industry for offloading of oil and gas. Loads on the mooring lines, vessel motions and wave elevations in the gap are among the most critical issues for this type of operations, and they are highly dependent on the hydrodynamic interaction between the vessels. On the other hand, there is limited experimental data available to validate numerical predictions of these hydrodynamic effects. This paper presents extensive experimental benchmark data, and a detailed uncertainty analysis of the results of two-body interaction model tests carried out in the towing tank of Memorial University, Canada. Sources of uncertainty were identified and quantified for 6-DOF motions, wave elevations in the gap between the two models, and drift forces. A combined experimental and numerical method was developed to quantify the uncertainties in model geometry, model mass properties, locations of models, and the set-up of the mooring system. Experimental results with associated uncertainties are compared with potential-flow solutions in the frequency domain. It was found that uncertainties due to the model geometry are negligible, however, those due to the model mass properties may be significant for roll motions. The uncertainty in gap leads to large uncertainties in all the measured results.