Background: The aim of this study is to draw a comprehensive picture of patients’ functional and critical health literacy and its association with socio-demographic variables and self-efficacy. We investigated the referrals to Isfahan health centers, in particular the dimensions of reading ability, numeracy and eHealth literacy using two different measures, NVS for the functional and the eHEALS for critical aspects. Methods: For testing individuals with low health literacy, the NVS is a reliable and quick screening tool. eHEALS helps to measure patients’ capabilities in Internet searches. Both of tools are validated in Persian. The measures were administered to a random sample (N = 384), which resembled Iran residents in terms, educational attainment and self-efficacy but not age and gender. Pearson’s correlation coefficient, χ2-test, independent t-test and regression were also used to assess the association between health literacy measures, self-efficacy and predictor variables. Results: More than 60% of our respondents had an inadequate or marginal level of health literacy with NVS, and with eHEALS, more than 50% were classified accordingly. NVS and eHEALS scores showed an association with higher education one of the predictors of health literacy. Higher eHEALS scores were associated with higher self-efficacy. eHEALS provides a valid self-reported assessment of patients’ eHealth literacy, and NVS provides a useful appraisal of patients’ functional health literacy. Conclusions: In our sample, more than 50% of patients had a low level of literacy. eHEALS provides a valid self-reported assessment of patients’ eHealth literacy, and NVS provides a useful appraisal of patients’ functional health literacy. Determining health literacy in patients leads to a better understanding of their perception, application and decision-making in health problems.