Contradictory data exist regarding optimal methods and instruments for intimate partner violence (IPV) screening in primary care settings. The purpose of this study was to determine the optimal method and screening instrument for IPV among men and women in a primary-care resident clinic. We conducted a cross-sectional study at an urban, academic, internal medicine residency continuity clinic in Connecticut among English or Spanish speaking adult patients. One group of patients ( n = 340) received a self-administered questionnaire (SAQ) containing the partner violence screen (PVS) and the Hurt, Insulted, Threatened or Screamed at Questionnaire (HITS). A second group (n = 126) was screened with PVS and HITS by their primary care providers during face-to-face (FTF) clinical encounters. Multivariable logistic regression models were used to determine the association between IPV prevalence and screening method (SAQ or FTF) after adjusting for socio-demographic effects. The overall IPV prevalence was 17.3% using the SAQ and 9.0% with FTF screening (p = 0.008). Patients receiving the SAQ were more likely to report IPV than those who were screened FTF (adjusted odds ratio [AOR]: 2.6, 95% confidence interval [CI]: 1.2-5.6). This effect persisted for women, who had a higher odds of IPV when screened through a SAQ than when screened FTF (AOR: 3.5, 95% CI: 1.4-8.6). Men did not differ in reporting IPV between methods: 11% with SAQ versus 9.4% FTF (p = 0.69). In internal medicine residency continuity clinics, a SAQ for IPV may result in higher disclosure and completion rates among female patients compared to FTF screening. Unique screening instruments and methods may be needed for men. (Contains 1 figure and 3 tables.)