Plasma D-dimers constitute a non-invasive diagnostic aid in excluding pulmonary embolism (PE) and deep vein thrombosis (DVT), well-established for outpatients. Our purpose was to define the best indications of plasma D-dimer testing in hospitalized patients with clinically suspected DVT and/or PE. In a retrospective case-control study we analyzed plasma D-dimers levels (measured by ELISA testing) of three hundred unselected hospitalized patients clinically suspected of DVT and/or PE. With a positive threshold of 0.5 mg/l, 3.2 % were false negatives (95 % confidence interval 1.1–5.3). True negatives were 21.2 % (95 % confidence interval 16.4–26) and divided as follows: 12.3 % from surgical patients, 20.6 % from medical patients and 45 % among emergency unit patients. Interestingly, 38 % true negatives were found among patients below the age of 80, with neither any malignant pathology nor a surgical context. Whereas plasma D-dimer testing in all hospitalized patients clinically suspected of DVTE would be time-consuming and costly, following the above prescription rule would be cost-effective and worthwhile to exclude DVTE at the hospital.