The factors associated with persistent instability of oral anticoagulant treatment (OAT) were investigated in a case-control study. The most unstable patients from 35 Italian anticoagulation clinics were matched with stable controls, for gender, age and OAT indication. Socio-demographic data, medical history, dietary and life habits, cytochrome P450 CYP2C9 variants, blood cell count, liver and renal functions were investigated. An 'Abbreviated Mental Test' (AMT) and a questionnaire to assess patient compliance to, and comprehension of, OAT indications and mechanisms were administered. An International Normalized Ratio (INR) above 4.5 was more frequently found in cases (n = 77) than controls (n = 80) (12.3% vs. 0.4%; P < 0.0001). The odds ratio for instability was significantly higher for: people who worked versus pensioners, acenocoumarol versus warfarin, and an insufficient score in the AMT and/or in the questionnaire. Cytochrome P450 CYP2C9 variants *1/*3 or *2/*3 or *3/*3 were more frequent among cases than controls (29.9% vs.15.0%; P = 0.042). No differences were observed as regards the other variables. In conclusion, we found that high intra-individual variability in OAT control was multifactorial, but poor OAT comprehension was prevalent.