This study (part of the nationwide French prevalence survey of 2001) was organized to investigate the prevalence and risk factors of nosocomial infections (NIs) and the resistant flora in patients hospitalized in rehabilitation units. Two hundred and eighty-six patients were included from two hospitals in the 'Hospices Civils de Lyon' group. Patients were classified into those with and without a spinal cord injury (SCI). Seventy-eight (27.3%) patients had an SCI. They were younger and more often characterized by a low Activity of Daily Life score, bladder incontinence and chronic respiratory disease. Urinary catheterization and mechanical ventilation were more common in these patients. The NI prevalence rate was higher in the SCI group (21.8% vs 4.3%, P<0.00001), particularly for urinary tract infections (UTIs, 19.2% vs 3.4%, P<0.00001). There was a positive relationship between the number of risk factors and NI acquisition. Multi-variate analysis showed that the only independent risk factor for NI acquisition was indwelling urinary catheterization [odds ratio (OR): 11.64, 95% confidence intervals (CI): 2.53-53.65, P=0.002]. Marginally significant factors were chronic kidney or liver disease (OR: 5.84, 95%CI: 0.80-42.68, P=0.082) and SCI (OR: 2.97, 95%CI: 0.61-14.60, P=0.179). The prevalence of antibiotic-resistant micro-organisms was high (nine cases of resistant organisms for 31 infection sites), but there were no differences between the groups. The high rate of NIs, especially UTIs, in SCI patients was not due to an independent effect of SCI but was probably due to the high number of risk factors. These high-risk patients need targeted NI surveillance.