Purpose The purpose of this paper is to establish practical guidelines for benchmarking eight total quality management (TQM) practices vital to pharmaceutical companies’ performance. The paper also proposes the use of an analytic total quality index (TQI) as a benchmarking tool and illustrates the importance and effectiveness of this benchmarking methodology by applying it in two comparative studies of three Jordanian pharmaceutical companies. Design/methodology/approach In order to achieve the above-mentioned purpose, the data were gathered through a questionnaire that was used to evaluate the gap between the ideal and current status of the quality management system and distributed to the quality units from three companies: pharmaceutical manufacturing company, a pharmaceutical manufacturing company working in the same field and a pharmaceutical service providing research services to a pharmaceutical manufacturing companies. And the mean differences between the current and ideal states for the eight critical TQM practices were compared for these two comparative studies using the t-test. Findings Each of the two comparisons reveals statistically significant differences regarding the perceptions of actual and ideal scores for manufacturing and service companies on five out of eight critical factors and, on two out of eight critical factors for manufacturing and manufacturing companies. Practical implications The pharmaceutical companies, regardless of whether they are manufacturing or service company, can adopt benchmarking techniques which were applied in this case study to improve their performance and their product/service quality. Originality/value The consequences of this research can support organization managers and policy makers in effectively benchmarking the identified TQM practices in their organizations using the proposed TQI benchmarking tool.