Background: Health literacy (HL) is linked to many health outcomes, including self-management of chronic diseases. The aim of this study was to assess the association of health literacy with the prevalence of obesity, arterial hypertension (AH), and type 2 diabetes mellitus (T2DM). Methods: This cross-sectional, single-center study included 500 patients (42.2% male and 57.8% females; median age, 63 years (interquartile range, 42–73)) hospitalized at General County Hospital in Požega, Croatia, between July and October 2020. The Short Assessment of Health Literacy for Croatian Adults (SAHLCA-50) questionnaire was used. Descriptive statistics (median with interquartile range (IQR), frequency, and percentages) and binary logistic regression were utilized. Results: Patients with AH had an inadequate level of health literacy as compared to those without AH (32 vs. 40 points; Mann–Whitney U test, p < 0.001). Patients with T2DM scored 31 points versus 39 points in patients without T2DM (Mann–Whitney U test, p < 0.001). Patients suffering from both AH and T2DM scored 31 points versus 33 points in those with either AH or T2DM and 41 points in patients without AH and T2DM (Kruskal–Wallis test, p < 0.001). There were no statistically significant differences in SAHLCA-50 scores according to the patient body mass index. Conclusions: An inadequate level of health literacy is significantly associated with AH and T2DM but not with obesity. Male gender, low level of education, rural place of residence, retirement, and older age are significant predictors of inadequate health literacy.