Little has changed in sexually transmitted infection (STI) epidemiology in Ireland since 2000. Three STIs comprise approximately 90% of notifications; ano-genital warts, Chlamydia trachomatis and non-specific urethritis. Our objective was to compare the risk factors for prevalent STIs in attendees at two genitourinary medicine clinics and examine the incidence of coinfection. Diagnostic, demographic and behavioural information on attendees at two clinics in southwest Ireland were collected from January 1999 to July 2009. Risk factors associated with first episodes of ano-genital warts, genital herpes simplex viral infection, non-specific urethritis and C. trachomatis were investigated. In all, 22,705 STI patients (mean age 27 years) received 26,824 diagnoses; 1628 had more than one infection. Ano-genital warts was most likely to be diagnosed with a coinfection. Having multiple partners was positively associated with a diagnosis of bacterial infection but not viral infection. Our large cohort outlines those at risk in the region, showing age and gender influences the risk and type of infection. Smoking, alcohol and drug use is also common, all regarded as markers of risk-taking behaviour. The younger the age, the higher the risk of acquiring infection, regardless of infection type. Prevention strategies that target youth, bacterial STIs and high-risk behaviour, including sexual, alcohol and drugs, may be effective in reducing STI incidence in Ireland.