BACKGROUND Older adults living in nursing homes (NH) are at high risk of developing influenza and pneumococcal infections. The objectives of this study were to describe vaccination coverage for influenza and pneumococcal among French NH residents and to investigate which NH structure- and organisation-related aspects could impact on vaccination in this population. METHODS This study is based on cross-sectional data from 175 French NHs (N=6275 residents), collected in May-July 2011. Residents' vaccination status (yes vs. no) against pneumococcal infection and seasonal influenza was recorded by the NH staff (on the basis of the resident's medical chart). Residents' health-related variables (e.g., co-morbidities) and information on NH structure and internal organisation were recorded by the NH staff. Mixed-effects logistic regressions were performed on influenza and pneumococcal vaccination separately. RESULTS Influenza vaccination coverage was high (n=5071, i.e., 80.8% of residents) and relatively well-distributed across NHs, whereas pneumococcal vaccination was low (n=1758, i.e., 28%) and highly variable across facilities. Mixed-effects logistic regressions confirmed that structural and organisational aspects related to the NH functioning impacted vaccination coverage. More precisely, living in a private for profit NH, living in NHs located in low-urban areas, and coordinating physician training increased the odds of receiving pneumococcal vaccine, whereas living in NHs located at high-urban areas decreased this odds. Moreover, the time spent by the coordinating physician in the NH increased the odds of receiving influenza vaccine. Prescriptions re-examination since resident's admission at the NH and the presence of an individualised health care project increased the odds of receiving both influenza and pneumococcal vaccines. CONCLUSIONS Our findings suggest that a more standardised approach is needed to improve vaccination coverage against pneumococcal infection in French NH residents.