Background Food shortage was associated with leprosy in two recent studies investigating the relation between socioeconomic factors and leprosy. Inadequate intake of nutrients due to food shortage may affect the immune system and influence the progression of infection to clinical leprosy. We aimed to identify possible differences in dietary intake between recently diagnosed leprosy patients and control subjects. Methods In a leprosy endemic area of Bangladesh, newly diagnosed leprosy patients and control subjects were interviewed about their socioeconomic situation, health and diet. Dietary intakes were recorded with a 24-hour recall, from which a Dietary Diversity Score (DDS) was calculated. Body Mass Index (BMI) was calculated and Household Food Insecurity Access Scale (HFIAS) was filled out for every participant. Using logistic regression, a univariate, block wise multivariate, and an integrated analysis were carried out. Results 52 leprosy cases and 100 control subjects were included. Food shortage was more common, dietary diversity was lower and household food insecurity was higher in the patient group. Patients consumed significantly less items from the DDS food groups 'Meat and fish' and 'Other fruits and vegetables.' Lower food expenditure per capita, lower BMI, lower DDS and absence of household food stocks are the main factors associated with an increased risk of having leprosy. Conclusion Low income families have only little money to spend on food and consequently have a low intake of highly nutritious non-rice foods such as meat, fish, milk, eggs, fruits and vegetables. Development of clinical leprosy could be explained by deficiencies of the nutrients that these foods normally provide.