Purpose To identify the risk of patients undergoing cataract surgery of having pathogenic conjunctival bacteria associated with their systemic co-morbidities. Methods Retrospective study of consecutive patients undergoing their first cataract operation from July 2005 to April 2010. Their preoperative conjunctival bacteria were cultured, identified, and classified in bacterial groups. Their co-morbidities were defined from their clinical data and the answers to systematic questions asked in the anaesthetic evaluation. The Microsoft Access databases of the two data sets were merged for carrying out the statistical analysis. Univariate association of each bacterial group with each co-morbidity was studied by using w 2 -test for categorical data and Student's t-test for continuous variables. Also, logistic regression models were used adjusting for age and sex. SPSS statistic programme, version 18 was used for all these analyses. Endophthalmitis cases in this surgical series were searched. Results In the 8333 selected patients, age was associated with increased conjunctival bacteria in all groups except for Streptococcus pneumoniae and Propionibacteriae. However, male sex was associated with these two groups and also with coagulase-negative Staphylococci, Corynebacterium xerosis, Staphylococcus aureus, and Gram-negative rods. After adjusting for age and sex, S. aureus was associated with diabetes, lung diseases, and renal and heart insufficiency; Gram-negative rods with smoking habit; Enterococci with diabetes; Streptococcus pneumoniae with kyphoscoliosis; and other Streptococci with diabetes and handicapped patients. Conclusion The more pathogenic conjunctival bacteria were more likely associated with patients' co-morbidities, such as diabetes, lung diseases, renal and heart insufficiency, kyphoscoliosis, and smoking habit, than the less pathogenic ones.