The study of calcineurin inhibitor (CNI) blood level variability to evaluate adherence in transplantation has improved over the years. The aim of our study was to assess factors associated with this variability using the coefficient of variation (CV). A cross-sectional sample of kidney recipients grafted for more than 1 year was recruited. We recorded clinical data, data from a clinical pharmacist interview and from six questionnaires measuring adherence, satisfaction, behaviours, beliefs, perception of the illness and social vulnerability. A total of 408 recipients were enrolled (61.2% male, mean age 54) and divided into two groups: low variability CV < 30% (n = 302), high variability CV ≥ 30% (n = 106). In univariate analysis, hospital-home distance, cyclosporine, time since transplantation and presence of discrepancies in drug regimen were associated with a greater risk of CV ≥ 30%. In contrast, tacrolimus QD conferred a lower risk of CV ≥ 30%. In multivariate analysis, only the presence of discrepancies remained significant: (OR 3.2 [1.21-9.01]; P = 0.022). Discrepancies in drug regimen appear as the main risk factor associated with CNI blood variability. The clinical pharmacist's input is an accurate and simple way of detecting non-adherence which is not revealed in self-report questionnaires.