An accurate diagnosis of glenohumeral joint (GHJ) instability is essential for an effective surgical intervention. There is presently no known comprehensive algorithm of clinical tests for the confirmation of the functional integrity of glenohumeral ligaments (GHLs). A validated computational GHL strain analyser was applied to a set of GHJ kinematics data from the literature to simulate 57 different physiological clinical examination manoeuvres. An algorithm that integrates the GHL pre-straining activities at the toe region of the stress–strain curve was developed for the quantification of ligament loading from prevailing strains. This was used to upgrade the strain analyser and applied to produce a matrix of the various GHL loadings and sensitivities during the manoeuvres. The investigation magnified the likely impact of anatomical variations of GHL attachments as possible causes of misdiagnoses during clinical examinations of GHJ dysfunction. This can serve as an assistive guide to ascertain the functional condition of a specific GHL during symptomatic clinical examinations.