Background: Understanding behavioral factors associated with low health literacy (HL) is relevant for health care providers to better support their patients’ health and adherence to preventive treatment. In this study, we aim to study associations between low HL and socio-demographic characteristics, medication-related perceptions and experience, as well as general psychological factors among patients aged 50–80 years. Methods: We used a cross-sectional survey design based on a representative group of 6,871 Danish citizens aged 50–80 years returning a web-based questionnaire with socio-demographic data added from a national registry. Chi-square tests were conducted to analyze associations between low HL and daily use of medication and self-rated health. Chi-square tests and binary logistic regression were conducted for analyzing data from respondents using prescribed medicines daily (N = 4,091). Results: Respondents with low HL were more often on daily medications (19 % [777/4,091] vs. 16 % [436/2,775]; P < 0.001) and were more likely to have poorer self-rated health (P < 0.001). Among patients on daily medications, low HL was significantly higher among men and those with lower educational attainment and lower family income. Low HL was independently and positively associated with perceptions that taking prescribed medicines daily is difficult and time-consuming, with forgetting to take prescribed medicines, and with lower satisfaction with life and poor self-assessed health. Conclusions: Our study provides information that patients aged 50–80 years with low HL are challenged on their adherence to treatment plans which is not only related to traditional sociodemographic factors but also on perceptions related to taking medication per se.