Molecular computing holds great promise for diagnosis and treatment of diseases at the molecular level; nevertheless, designing molecular logic gates to operate programmably and autonomously for molecular diagnostics still remains challenging. We designed logic gates on DNA Origami for microRNA analysis. As a demonstration, two indicators of heart failure, microRNA-21 and microRNA-195, were selected as the logic inputs. The logic gates contain two main modules: computation module and output module, performing in a single DNA Origami nanostructure. The computation module recognizes disease indicators, while the output module display different nanoscale symbols, “+” (positive) or “–” (negative), depending on the computing results. We demonstrated that the molecular logic gates worked well with single and two input combinations.